Notice (8): Undefined variable: source_groups_information [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ), 'data_type' => 'gene_family', 'gf_id' => 'HOM05M001727', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05M001727' ), 'all_species' => array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ) $data_type = 'gene_family' $gf_id = 'HOM05M001727' $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05M001727' ) $all_species = array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'HOM05M001727' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 149
<label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
<label>Source(s)</label>
<select class='form form-select' name='ontology_source_group' id='ontology_source_group'>
<?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
$viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ), 'data_type' => 'gene_family', 'gf_id' => 'HOM05M001727', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05M001727' ), 'all_species' => array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ) $data_type = 'gene_family' $gf_id = 'HOM05M001727' $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05M001727' ) $all_species = array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'HOM05M001727' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' )
include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 149
Notice (8): Trying to access array offset on value of type null [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ), 'data_type' => 'gene_family', 'gf_id' => 'HOM05M001727', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05M001727' ), 'all_species' => array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ) $data_type = 'gene_family' $gf_id = 'HOM05M001727' $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05M001727' ) $all_species = array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'HOM05M001727' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 149
Warning (2): Invalid argument supplied for foreach() [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ), 'data_type' => 'gene_family', 'gf_id' => 'HOM05M001727', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05M001727' ), 'all_species' => array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'HOM05M001727', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 3, 'num_colinearity_with_dating_runs' => (int) 2, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' ) ), 'genes' => array( 'AET0Gv20048400' => 'ata', 'AET2Gv21020400' => 'ata', 'AET2Gv21020700' => 'ata', 'AET2Gv21020800' => 'ata', 'AET5Gv20597200' => 'ata', 'AET5Gv20597400' => 'ata', 'AET5Gv20597500' => 'ata', 'AET5Gv20597700' => 'ata', 'AET5Gv20598600' => 'ata', 'AET5Gv20598700' => 'ata', 'AT3G07870' => 'ath', 'Bradi4g01502' => 'bdi', 'Bradi4g01506' => 'bdi', 'Bradi4g01513' => 'bdi', 'Bradi4g33137' => 'bdi', 'Bradi4g33144' => 'bdi', 'Bradi4g33147' => 'bdi', 'Bradi4g33152' => 'bdi', 'CDE05G3368' => 'cde', 'Dexi2A01G0020840' => 'dex', 'Dexi2A01G0020850' => 'dex', 'Dexi2B01G0019540' => 'dex', 'Dexi2B01G0019550' => 'dex', 'EJB05_43446' => 'ecu', 'EJB05_43447' => 'ecu', 'GWHGAORA007754' => 'cpu', 'GWHGAORA007776' => 'cpu', 'GWHGAORA007777' => 'cpu', 'GWHGAORA007780' => 'cpu', 'GWHGAORA047992' => 'cpu', 'GWHGAORA047993' => 'cpu', 'GWHGAORA047995' => 'cpu', 'GWHGAORA047996' => 'cpu', 'GWHGAORA047997' => 'cpu', 'GWHGAORA047998' => 'cpu', 'GWHGAORA053807' => 'cpu', 'GWHGAORA053902' => 'cpu', 'GWHGASIY010748' => 'sce', 'GWHGASIY019446' => 'sce', 'GWHGASIY026715' => 'sce', 'GWHGASIY026716' => 'sce', 'GWHGASIY026717' => 'sce', 'GWHGASIY026718' => 'sce', 'GWHGASIY026719' => 'sce', 'GWHGASIY026720' => 'sce', 'GWHGASIY026721' => 'sce', 'GWHGASIY026722' => 'sce', 'GWHGASIY026723' => 'sce', 'GWHGASIY026725' => 'sce', 'GWHGAZTO051946' => 'oal', 'GWHGAZTO051947' => 'oal', 'GWHGAZTO098369' => 'oal', 'GWHGAZTO098370' => 'oal', 'GWHGAZTO098715' => 'oal', 'Horvu_MOREX_2H01G637500' => 'hvu', 'Horvu_MOREX_5H01G413200' => 'hvu', 'Horvu_MOREX_5H01G413400' => 'hvu', 'Misin03G190200' => 'msi', 'Misin03G190300' => 'msi', 'Misin04G221600' => 'msi', 'Misin04G221700' => 'msi', 'Misin04G221800' => 'msi', 'Misin04G222000' => 'msi', 'Misin04G222200' => 'msi', 'OB09G20540' => 'obr', 'OB09G20550' => 'obr', 'Os09g0479000' => 'osa', 'Os09g0479100' => 'osa', 'Os09g0517800' => 'osa', 'OsKitaake09g139000' => 'osak', 'OsKitaake09g139100' => 'osak', 'OsKitaake09g166400' => 'osak', 'OsR498G0917689100.01' => 'osaindica', 'OsR498G0917689300.01' => 'osaindica', 'OsR498G0917804100.01' => 'osaindica', 'Ot_Chr2_g05574' => 'oth', 'Ot_Chr2_g05577' => 'oth', 'Ot_Chr2_g05578' => 'oth', 'Ot_Chr2_gn33492' => 'oth', 'p5.00_sc00001_p0948' => 'egu', 'Pahal.2G305101' => 'pha', 'Pahal.2G305200' => 'pha', 'PH02Gene01314' => 'ped', 'PH02Gene05975' => 'ped', 'Potri.001G129400' => 'ptr', 'Potri.001G224200' => 'ptr', 'Potri.002G223000' => 'ptr', 'Potri.008G215901' => 'ptr', 'Potri.008G216000' => 'ptr', 'Potri.013G104100' => 'ptr', 'Potri.014G162600' => 'ptr', 'Seita.2G245400' => 'sit', 'Sevir.2G256000' => 'svi', 'Sobic.002G239300' => 'sbi', 'Sobic.002G239400' => 'sbi', 'Sobic.002G239450' => 'sbi', 'Sobic.002G239601' => 'sbi', 'Solyc02g072423.1' => 'sly', 'Solyc02g082320.1' => 'sly', 'Solyc07g055020.3' => 'sly', 'Solyc10g009450.1' => 'sly', 'Solyc12g006130.3' => 'sly', 'Sspon.02G0012200-1A' => 'ssp', 'Sspon.02G0012200-1P' => 'ssp', 'Sspon.02G0012200-2D' => 'ssp', 'Sspon.02G0012200-2P' => 'ssp', 'Sspon.02G0012250-1A' => 'ssp', 'Sspon.02G0012250-2D' => 'ssp', 'Sspon.02G0048220-1C' => 'ssp', 'Sspon.02G0048230-1C' => 'ssp', 'TraesCS2B03G1222200' => 'tae', 'TraesCS2D03G1033800' => 'tae', 'TraesCS5A03G0633900' => 'tae', 'TraesCS5A03G0634200' => 'tae', 'TraesCS5A03G0635000' => 'tae', 'TraesCS5A03G0635100' => 'tae', 'TraesCS5A03G0635300' => 'tae', 'TraesCS5A03G0635600' => 'tae', 'TraesCS5A03G0635700' => 'tae', 'TraesCS5A03G0635800' => 'tae', 'TraesCS5B03G0656900' => 'tae', 'TraesCS5B03G0657000' => 'tae', 'TraesCS5B03G0657400' => 'tae', 'TraesCS5B03G0657500' => 'tae', 'TraesCS5B03G0657800' => 'tae', 'TraesCS5B03G0657900' => 'tae', 'TraesCS5B03G0658000' => 'tae', 'TraesCS5B03G0658200' => 'tae', 'TraesCS5B03G0658300' => 'tae', 'TraesCS5B03G0658500' => 'tae', 'TraesCS5D03G0601100' => 'tae', 'TraesCS5D03G0601300' => 'tae', 'TraesCS5D03G0601500' => 'tae', 'TraesCS5D03G0601600' => 'tae', 'TraesCS5D03G0601700' => 'tae', 'TraesCS5D03G0601800' => 'tae', 'TraesCS5D03G0601900' => 'tae', 'TraesCS5D03G0602000' => 'tae', 'TraesCS5D03G0602200' => 'tae', 'TraesCS5D03G0602500' => 'tae', 'TraesCS5D03G0704900' => 'tae', 'TRIDC5AG039550' => 'tdi', 'TRIDC5AG039570' => 'tdi', 'TRIDC5AG039600' => 'tdi', 'TRIDC5AG039610' => 'tdi', 'TRIDC5AG039620' => 'tdi', 'TRIDC5AG039650' => 'tdi', 'TRIDC5AG039660' => 'tdi', 'TRIDC5AG039670' => 'tdi', 'TRIDC5BG042010' => 'tdi', 'TRIDC5BG042020' => 'tdi', 'TRIDC5BG042040' => 'tdi', 'TRIDC5BG042050' => 'tdi', 'TRIDC5BG042070' => 'tdi', 'TRIDC5BG042080' => 'tdi', 'TRIDC5BG042120' => 'tdi', 'TRIDC5BG042130' => 'tdi', 'TRITD2Bv1G222820' => 'ttu', 'TRITD5Av1G155510' => 'ttu', 'TRITD5Av1G155540' => 'ttu', 'TRITD5Av1G155700' => 'ttu', 'TRITD5Av1G155720' => 'ttu', 'TRITD5Av1G155730' => 'ttu', 'TRITD5Av1G155750' => 'ttu', 'TRITD5Av1G155780' => 'ttu', 'TRITD5Bv1G144340' => 'ttu', 'TRITD5Bv1G144360' => 'ttu', 'TRITD5Bv1G144380' => 'ttu', 'TRITD5Bv1G144390' => 'ttu', 'TRITD5Bv1G144400' => 'ttu', 'TRITD5Bv1G144410' => 'ttu', 'TRITD5Bv1G144420' => 'ttu', 'TRITD5Bv1G144430' => 'ttu', 'TRITD5Bv1G144440' => 'ttu', 'V3.Lp_chr3_0G19228' => 'lpe', 'V3.Lp_chr3_0G21352' => 'lpe', 'V3.Lp_chr3_0G21356' => 'lpe', 'V3.Lp_chr3_0G21358' => 'lpe', 'V3.Lp_chr5_0G10764' => 'lpe', 'V3.Lp_chr5_0G14940' => 'lpe', 'V3.Lp_chr5_0G15046' => 'lpe', 'V3.Lp_chr5_0G15054' => 'lpe', 'V3.Lp_chr5_0G15056' => 'lpe', 'V3.Lp_chr5_0G15066' => 'lpe', 'V3.Lp_chr5_0G15068' => 'lpe', 'V3.Lp_chr5_0G15070' => 'lpe', 'V3.Lp_chr5_0G15082' => 'lpe', 'V3.Lp_chr5_0G15084' => 'lpe', 'V3.Lp_chr5_0G15094' => 'lpe', 'V3.Lp_chr5_0G15904' => 'lpe', 'V3.Lp_chr5_0G17168' => 'lpe', 'V3.Lp_chr5_0G17262' => 'lpe', 'V3.Lp_chr5_0G18272' => 'lpe', 'V3.Lp_chr7_0.1G4860' => 'lpe', 'Zjn_sc00018.1.g02480.1.am.mk' => 'zjn', 'Zjn_sc00018.1.g02500.1.am.mkhc' => 'zjn', 'Zjn_sc00018.1.g02510.1.cf.mkhc' => 'zjn', 'Zjn_sc00039.1.g00030.1.sm.mkhc' => 'zjn', 'Zm00001eb101520' => 'zma', 'Zm00007a00043882' => 'zma-b104' ) ) $data_type = 'gene_family' $gf_id = 'HOM05M001727' $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05M001727' ) $all_species = array( 'ata' => array( 'species' => 'ata', 'common_name' => 'Aegilops tauschii', 'tax_id' => '37682', 'version' => 'Aet V4.0' ), 'asa' => array( 'species' => 'asa', 'common_name' => 'Allium sativum', 'tax_id' => '4682', 'version' => 'V1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aco' => array( 'species' => 'aco', 'common_name' => 'Ananas comosus', 'tax_id' => '4615', 'version' => 'JGI v3.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'aof' => array( 'species' => 'aof', 'common_name' => 'Asparagus officinalis', 'tax_id' => '4686', 'version' => 'v1.1' ), 'bdi' => array( 'species' => 'bdi', 'common_name' => 'Brachypodium distachyon', 'tax_id' => '15368', 'version' => 'JGI v3.2' ), 'calsi' => array( 'species' => 'calsi', 'common_name' => 'Calamus simplicifolius', 'tax_id' => '746888', 'version' => 'v1.0' ), 'cpu' => array( 'species' => 'cpu', 'common_name' => 'Cenchrus purpureus', 'tax_id' => '154765', 'version' => 'v1.0' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'dex' => array( 'species' => 'dex', 'common_name' => 'Digitaria exilis', 'tax_id' => '1010633', 'version' => 'Dexi_CM05836 v1' ), 'ddu' => array( 'species' => 'ddu', 'common_name' => 'Dioscorea dumetorum', 'tax_id' => '167584', 'version' => 'Trifoliate Yam v1.0' ), 'egu' => array( 'species' => 'egu', 'common_name' => 'Elaeis guineensis', 'tax_id' => '51953', 'version' => 'EG5.1' ), 'ecu' => array( 'species' => 'ecu', 'common_name' => 'Eragrostis curvula', 'tax_id' => '38414', 'version' => 'CERZOS_E.curvula1.0' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'hvu' => array( 'species' => 'hvu', 'common_name' => 'Hordeum vulgare', 'tax_id' => '4513', 'version' => 'Morex v2' ), 'lpe' => array( 'species' => 'lpe', 'common_name' => 'Lolium perenne', 'tax_id' => '4522', 'version' => '2.6.1-v3' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'msi' => array( 'species' => 'msi', 'common_name' => 'Miscanthus sinensis', 'tax_id' => '62337', 'version' => 'v7.1' ), 'mac' => array( 'species' => 'mac', 'common_name' => 'Musa acuminata', 'tax_id' => '4641', 'version' => 'Banana Genome v2.0' ), 'oth' => array( 'species' => 'oth', 'common_name' => 'Oropetium thomaeum', 'tax_id' => '1148796', 'version' => 'COGE v2.0' ), 'oal' => array( 'species' => 'oal', 'common_name' => 'Oryza alta', 'tax_id' => '52545', 'version' => 'OAv1' ), 'obr' => array( 'species' => 'obr', 'common_name' => 'Oryza brachyantha', 'tax_id' => '4533', 'version' => 'Ensembl Plants v1.4b' ), 'osak' => array( 'species' => 'osak', 'common_name' => 'Oryza sativa Kitaake', 'tax_id' => '4530', 'version' => 'V3.2' ), 'osaindica' => array( 'species' => 'osaindica', 'common_name' => 'Oryza sativa ssp. indica', 'tax_id' => '39946', 'version' => 'MBKBASE v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pha' => array( 'species' => 'pha', 'common_name' => 'Panicum hallii', 'tax_id' => '206008', 'version' => 'JGI v3.2' ), 'ped' => array( 'species' => 'ped', 'common_name' => 'Phyllostachys edulis', 'tax_id' => '38705', 'version' => 'GigaDBv2.0' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ssp' => array( 'species' => 'ssp', 'common_name' => 'Saccharum spontaneum', 'tax_id' => '62335', 'version' => 'v20190103' ), 'sce' => array( 'species' => 'sce', 'common_name' => 'Secale cereale', 'tax_id' => '4550', 'version' => 'Rye v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sit' => array( 'species' => 'sit', 'common_name' => 'Setaria italica', 'tax_id' => '4555', 'version' => 'JGI v2.2' ), 'svi' => array( 'species' => 'svi', 'common_name' => 'Setaria viridis', 'tax_id' => '4556', 'version' => 'Phytozome v2.1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'sbi' => array( 'species' => 'sbi', 'common_name' => 'Sorghum bicolor', 'tax_id' => '4558', 'version' => 'JGI v3.1' ), 'spo' => array( 'species' => 'spo', 'common_name' => 'Spirodela polyrhiza', 'tax_id' => '29656', 'version' => 'JGI v2.0' ), 'tae' => array( 'species' => 'tae', 'common_name' => 'Triticum aestivum', 'tax_id' => '4565', 'version' => 'IWGSCv2.1' ), 'tdi' => array( 'species' => 'tdi', 'common_name' => 'Triticum dicoccoides', 'tax_id' => '85692', 'version' => 'Ensembl' ), 'ttu' => array( 'species' => 'ttu', 'common_name' => 'Triticum turgidum', 'tax_id' => '4567', 'version' => 'v1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays B73', 'tax_id' => '4577', 'version' => 'NAM v5.0' ), 'zma-b104' => array( 'species' => 'zma-b104', 'common_name' => 'Zea mays B104', 'tax_id' => '4577', 'version' => 'v1.0' ), 'zosmarina' => array( 'species' => 'zosmarina', 'common_name' => 'Zostera marina', 'tax_id' => '29655', 'version' => 'v3.1' ), 'zjn' => array( 'species' => 'zjn', 'common_name' => 'Zoysia japonica ssp. nagirizaki', 'tax_id' => '309978', 'version' => 'Zoysia Genome Database v1.1' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'HOM05M001727' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'HOM05M001727' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 149