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These files contains the overview of all species in this PLAZA instance.
Additionally, extra information such as naming conventions, source information, version information, publication information, etc. are also provided.
SpeciesData File
All Species species_information.csv.gz (1.58 KB)

These files contain, per species, the structural annotation for each gene in this PLAZA instance in CSV format.
This includes gene identifier information, coordinate information, strand information, etc.
SpeciesAll transcriptsSelected transcript
Phaeodactylum tricornutum annotation.all_transcripts.ptri.csv.gz (5.61 MB) annotation.selected_transcript.ptri.csv.gz (5.61 MB)
Thalassiosira pseudonana annotation.all_transcripts.tps.csv.gz (5.51 MB) annotation.selected_transcript.tps.csv.gz (5.50 MB)
Thalassiosira oceanica annotation.all_transcripts.tho.csv.gz (11.86 MB) annotation.selected_transcript.tho.csv.gz (11.86 MB)
Pseudo-nitzschia multiseries annotation.all_transcripts.psm.csv.gz (7.23 MB) annotation.selected_transcript.psm.csv.gz (7.23 MB)
Fistulifera solaris annotation.all_transcripts.fso.csv.gz (9.61 MB) annotation.selected_transcript.fso.csv.gz (9.61 MB)
Fragilariopsis cylindrus annotation.all_transcripts.fcy.csv.gz (8.22 MB) annotation.selected_transcript.fcy.csv.gz (8.22 MB)
Cyclotella cryptica annotation.all_transcripts.cycr.csv.gz (8.91 MB) annotation.selected_transcript.cycr.csv.gz (8.91 MB)
Aureococcus anophagefferens annotation.all_transcripts.aan.csv.gz (5.23 MB) annotation.selected_transcript.aan.csv.gz (5.23 MB)
Ectocarpus siliculosus annotation.all_transcripts.esi.csv.gz (9.49 MB) annotation.selected_transcript.esi.csv.gz (9.48 MB)
Nannochloropsis gaditana annotation.all_transcripts.nga.csv.gz (4.36 MB) annotation.selected_transcript.nga.csv.gz (4.16 MB)
Homo sapiens annotation.all_transcripts.hom.csv.gz (51.43 MB) annotation.selected_transcript.hom.csv.gz (24.93 MB)
Drosophila melanogaster annotation.all_transcripts.drm.csv.gz (13.49 MB) annotation.selected_transcript.drm.csv.gz (7.97 MB)
Caenorhabditis elegans annotation.all_transcripts.cel.csv.gz (13.48 MB) annotation.selected_transcript.cel.csv.gz (10.38 MB)
Saccharomyces cerevisiae strain S288C annotation.all_transcripts.sac.csv.gz (2.70 MB) annotation.selected_transcript.sac.csv.gz (2.70 MB)
Schizosaccharomyces pombe annotation.all_transcripts.scp.csv.gz (2.86 MB) annotation.selected_transcript.scp.csv.gz (2.86 MB)
Arabidopsis thaliana annotation.all_transcripts.ath.csv.gz (17.56 MB) annotation.selected_transcript.ath.csv.gz (14.66 MB)
Cyanidioschyzon merolae annotation.all_transcripts.cme.csv.gz (2.33 MB) annotation.selected_transcript.cme.csv.gz (2.33 MB)
Chondrus crispus annotation.all_transcripts.ccr.csv.gz (3.27 MB) annotation.selected_transcript.ccr.csv.gz (3.22 MB)
Galdieria sulphuraria annotation.all_transcripts.gsu.csv.gz (2.78 MB) annotation.selected_transcript.gsu.csv.gz (2.75 MB)
Emiliania huxleyi annotation.all_transcripts.emh.csv.gz (12.78 MB) annotation.selected_transcript.emh.csv.gz (12.78 MB)
Paramecium tetraurelia annotation.all_transcripts.pte.csv.gz (16.94 MB) annotation.selected_transcript.pte.csv.gz (16.94 MB)
Seminavis robusta annotation.all_transcripts.sro.csv.gz (16.76 MB) annotation.selected_transcript.sro.csv.gz (16.28 MB)
Synedra acus annotation.all_transcripts.sya.csv.gz (10.36 MB) annotation.selected_transcript.sya.csv.gz (10.34 MB)
Physcomitrella patens annotation.all_transcripts.ppa.csv.gz (24.81 MB) annotation.selected_transcript.ppa.csv.gz (12.53 MB)
Chlamydomonas reinhardtii annotation.all_transcripts.cre.csv.gz (13.35 MB) annotation.selected_transcript.cre.csv.gz (12.18 MB)
Pseudo-nitzschia multistriata annotation.all_transcripts.pmu.csv.gz (6.12 MB) annotation.selected_transcript.pmu.csv.gz (6.05 MB)

These files contain, per species, the structural annotation for each gene in this PLAZA instance in GFF format.
This includes gene identifier information, coordinate information, strand information, etc.
SpeciesAll transcriptsSelected transcript
All featuresExon features onlyAll featuresExon features only
Phaeodactylum tricornutum File 1 (984.21 KB) File 2 (797.76 KB) File 3 (983.90 KB) File 4 (797.90 KB)
Thalassiosira pseudonana File 1 (1.03 MB) File 2 (833.24 KB) File 3 (1.03 MB) File 4 (833.26 KB)
Thalassiosira oceanica File 1 (2.87 MB) File 2 (2.24 MB) File 3 (2.87 MB) File 4 (2.24 MB)
Pseudo-nitzschia multiseries File 1 (1.83 MB) File 2 (1.31 MB) File 3 (1.83 MB) File 4 (1.31 MB)
Fistulifera solaris File 1 (664.20 KB) File 2 (574.97 KB) File 3 (1.28 MB) File 4 (1011.21 KB)
Fragilariopsis cylindrus File 1 (1.71 MB) File 2 (1.25 MB) File 3 (1.71 MB) File 4 (1.25 MB)
Cyclotella cryptica File 1 (1.67 MB) File 2 (1.31 MB) File 3 (1.67 MB) File 4 (1.31 MB)
Aureococcus anophagefferens File 1 (1.04 MB) File 2 (795.31 KB) File 3 (1.04 MB) File 4 (795.27 KB)
Ectocarpus siliculosus File 1 (3.59 MB) File 2 (2.46 MB) File 3 (3.59 MB) File 4 (2.46 MB)
Nannochloropsis gaditana File 1 (941.37 KB) File 2 (728.24 KB) File 3 (915.95 KB) File 4 (713.09 KB)
Homo sapiens File 1 (22.12 MB) File 2 (17.37 MB) File 3 (9.00 MB) File 4 (7.69 MB)
Drosophila melanogaster File 1 (3.72 MB) File 2 (2.78 MB) File 3 (2.15 MB) File 4 (1.79 MB)
Caenorhabditis elegans File 1 (5.55 MB) File 2 (4.37 MB) File 3 (4.37 MB) File 4 (3.64 MB)
Saccharomyces cerevisiae strain S288C File 1 (451.28 KB) File 2 (386.19 KB) File 3 (451.29 KB) File 4 (385.90 KB)
Schizosaccharomyces pombe File 1 (515.07 KB) File 2 (425.21 KB) File 3 (515.01 KB) File 4 (425.11 KB)
Arabidopsis thaliana File 1 (5.70 MB) File 2 (3.72 MB) File 3 (4.65 MB) File 4 (3.15 MB)
Cyanidioschyzon merolae File 1 (253.61 KB) File 2 (207.49 KB) File 3 (253.61 KB) File 4 (207.50 KB)
Chondrus crispus File 1 (656.92 KB) File 2 (529.95 KB) File 3 (644.09 KB) File 4 (518.96 KB)
Galdieria sulphuraria File 1 (703.02 KB) File 2 (538.78 KB) File 3 (697.28 KB) File 4 (534.25 KB)
Emiliania huxleyi File 1 (4.04 MB) File 2 (3.12 MB) File 3 (4.04 MB) File 4 (3.12 MB)
Paramecium tetraurelia File 1 (3.94 MB) File 2 (3.03 MB) File 3 (3.94 MB) File 4 (3.03 MB)
Seminavis robusta File 1 (3.03 MB) File 2 (1.98 MB) File 3 (3.00 MB) File 4 (1.97 MB)
Synedra acus File 1 (1.98 MB) File 2 (1.50 MB) File 3 (1.98 MB) File 4 (1.50 MB)
Physcomitrella patens File 1 (12.61 MB) File 2 (7.49 MB) File 3 (5.57 MB) File 4 (3.71 MB)
Chlamydomonas reinhardtii File 1 (4.61 MB) File 2 (2.99 MB) File 3 (4.30 MB) File 4 (2.83 MB)
Pseudo-nitzschia multistriata File 1 (1.30 MB) File 2 (752.59 KB) File 3 (1.29 MB) File 4 (747.97 KB)

These files contain the mapping between genes and transcripts.
SpeciesAll transcriptsSelected transcript
Phaeodactylum tricornutum transcript_mapping.all_transcripts.ptri.csv.gz (61.00 KB) transcript_mapping.selected_transcript.ptri.csv.gz (61.00 KB)
Thalassiosira pseudonana transcript_mapping.all_transcripts.tps.csv.gz (59.15 KB) transcript_mapping.selected_transcript.tps.csv.gz (59.15 KB)
Thalassiosira oceanica transcript_mapping.all_transcripts.tho.csv.gz (158.99 KB) transcript_mapping.selected_transcript.tho.csv.gz (159.00 KB)
Pseudo-nitzschia multiseries transcript_mapping.all_transcripts.psm.csv.gz (92.18 KB) transcript_mapping.selected_transcript.psm.csv.gz (92.19 KB)
Fistulifera solaris transcript_mapping.all_transcripts.fso.csv.gz (100.57 KB) transcript_mapping.selected_transcript.fso.csv.gz (100.49 KB)
Fragilariopsis cylindrus transcript_mapping.all_transcripts.fcy.csv.gz (106.72 KB) transcript_mapping.selected_transcript.fcy.csv.gz (106.71 KB)
Cyclotella cryptica transcript_mapping.all_transcripts.cycr.csv.gz (97.02 KB) transcript_mapping.selected_transcript.cycr.csv.gz (97.02 KB)
Aureococcus anophagefferens transcript_mapping.all_transcripts.aan.csv.gz (50.63 KB) transcript_mapping.selected_transcript.aan.csv.gz (50.64 KB)
Ectocarpus siliculosus transcript_mapping.all_transcripts.esi.csv.gz (92.40 KB) transcript_mapping.selected_transcript.esi.csv.gz (92.40 KB)
Nannochloropsis gaditana transcript_mapping.all_transcripts.nga.csv.gz (57.32 KB) transcript_mapping.selected_transcript.nga.csv.gz (53.63 KB)
Homo sapiens transcript_mapping.all_transcripts.hom.csv.gz (1.10 MB) transcript_mapping.selected_transcript.hom.csv.gz (393.38 KB)
Drosophila melanogaster transcript_mapping.all_transcripts.drm.csv.gz (171.65 KB) transcript_mapping.selected_transcript.drm.csv.gz (93.77 KB)
Caenorhabditis elegans transcript_mapping.all_transcripts.cel.csv.gz (331.98 KB) transcript_mapping.selected_transcript.cel.csv.gz (274.86 KB)
Saccharomyces cerevisiae strain S288C transcript_mapping.all_transcripts.sac.csv.gz (34.57 KB) transcript_mapping.selected_transcript.sac.csv.gz (34.57 KB)
Schizosaccharomyces pombe transcript_mapping.all_transcripts.scp.csv.gz (32.78 KB) transcript_mapping.selected_transcript.scp.csv.gz (32.77 KB)
Arabidopsis thaliana transcript_mapping.all_transcripts.ath.csv.gz (205.75 KB) transcript_mapping.selected_transcript.ath.csv.gz (169.58 KB)
Cyanidioschyzon merolae transcript_mapping.all_transcripts.cme.csv.gz (23.17 KB) transcript_mapping.selected_transcript.cme.csv.gz (23.17 KB)
Chondrus crispus transcript_mapping.all_transcripts.ccr.csv.gz (49.63 KB) transcript_mapping.selected_transcript.ccr.csv.gz (48.27 KB)
Galdieria sulphuraria transcript_mapping.all_transcripts.gsu.csv.gz (38.25 KB) transcript_mapping.selected_transcript.gsu.csv.gz (37.82 KB)
Emiliania huxleyi transcript_mapping.all_transcripts.emh.csv.gz (187.92 KB) transcript_mapping.selected_transcript.emh.csv.gz (187.93 KB)
Paramecium tetraurelia transcript_mapping.all_transcripts.pte.csv.gz (193.52 KB) transcript_mapping.selected_transcript.pte.csv.gz (193.53 KB)
Seminavis robusta transcript_mapping.all_transcripts.sro.csv.gz (172.16 KB) transcript_mapping.selected_transcript.sro.csv.gz (162.11 KB)
Synedra acus transcript_mapping.all_transcripts.sya.csv.gz (132.79 KB) transcript_mapping.selected_transcript.sya.csv.gz (131.99 KB)
Physcomitrella patens transcript_mapping.all_transcripts.ppa.csv.gz (371.52 KB) transcript_mapping.selected_transcript.ppa.csv.gz (174.25 KB)
Chlamydomonas reinhardtii transcript_mapping.all_transcripts.cre.csv.gz (107.54 KB) transcript_mapping.selected_transcript.cre.csv.gz (97.78 KB)
Pseudo-nitzschia multistriata transcript_mapping.all_transcripts.pmu.csv.gz (63.46 KB) transcript_mapping.selected_transcript.pmu.csv.gz (62.46 KB)

These files contain, per species, the gene identifiers and descriptions available for each gene in this PLAZA instance.
Many genes are known by their aliases (e.g. E2F3 for AT2G36010). These files contain this kind of identifier mappings.
SpeciesIdentifiersDescriptions
Phaeodactylum tricornutum id_conversion.ptri.csv.gz (275.93 KB) gene_description.ptri.csv.gz (148.33 KB)
Thalassiosira pseudonana id_conversion.tps.csv.gz (191.25 KB) gene_description.tps.csv.gz (189.27 KB)
Thalassiosira oceanica id_conversion.tho.csv.gz (583.24 KB) gene_description.tho.csv.gz (308.83 KB)
Pseudo-nitzschia multiseries id_conversion.psm.csv.gz (311.45 KB) gene_description.psm.csv.gz (130.67 KB)
Fistulifera solaris id_conversion.fso.csv.gz (99.91 KB) gene_description.fso.csv.gz (199.96 KB)
Fragilariopsis cylindrus id_conversion.fcy.csv.gz (327.22 KB) gene_description.fcy.csv.gz (149.94 KB)
Cyclotella cryptica id_conversion.cycr.csv.gz (190.75 KB) gene_description.cycr.csv.gz (157.90 KB)
Aureococcus anophagefferens id_conversion.aan.csv.gz (174.28 KB) gene_description.aan.csv.gz (2.40 KB)
Ectocarpus siliculosus id_conversion.esi.csv.gz (212.24 KB) gene_description.esi.csv.gz (291.00 B)
Nannochloropsis gaditana id_conversion.nga.csv.gz (107.20 KB) gene_description.nga.csv.gz (99.54 KB)
Homo sapiens id_conversion.hom.csv.gz (1.84 MB) gene_description.hom.csv.gz (520.26 KB)
Drosophila melanogaster id_conversion.drm.csv.gz (632.30 KB) gene_description.drm.csv.gz (77.31 KB)
Caenorhabditis elegans id_conversion.cel.csv.gz (619.22 KB) gene_description.cel.csv.gz (213.70 KB)
Saccharomyces cerevisiae strain S288C id_conversion.sac.csv.gz (240.51 KB) gene_description.sac.csv.gz (416.02 KB)
Schizosaccharomyces pombe id_conversion.scp.csv.gz (113.48 KB) gene_description.scp.csv.gz (82.09 KB)
Arabidopsis thaliana id_conversion.ath.csv.gz (388.21 KB) gene_description.ath.csv.gz (952.12 KB)
Cyanidioschyzon merolae id_conversion.cme.csv.gz (27.40 KB) gene_description.cme.csv.gz (74.48 KB)
Chondrus crispus id_conversion.ccr.csv.gz (155.27 KB) gene_description.ccr.csv.gz (22.66 KB)
Galdieria sulphuraria id_conversion.gsu.csv.gz (112.14 KB) gene_description.gsu.csv.gz (64.99 KB)
Emiliania huxleyi id_conversion.emh.csv.gz (605.19 KB) gene_description.emh.csv.gz (150.11 KB)
Paramecium tetraurelia id_conversion.pte.csv.gz (591.03 KB) gene_description.pte.csv.gz (2.15 KB)
Seminavis robusta id_conversion.sro.csv.gz (163.42 KB) gene_description.sro.csv.gz (369.35 KB)
Synedra acus id_conversion.sya.csv.gz (150.67 KB) gene_description.sya.csv.gz (208.14 KB)
Physcomitrella patens id_conversion.ppa.csv.gz (825.54 KB) gene_description.ppa.csv.gz (305.00 B)
Chlamydomonas reinhardtii id_conversion.cre.csv.gz (473.50 KB) gene_description.cre.csv.gz (191.52 KB)
Pseudo-nitzschia multistriata id_conversion.pmu.csv.gz (218.62 KB) gene_description.pmu.csv.gz (108.02 KB)

These files contain, per species, the functional annotation of the genes within this PLAZA instance.

This information is limited to the annotation of the genes.
For the associated ontologies (such as parent-child relationships between the various terms), you can find the necessary information here:
SpeciesGene OntologyInterProMapMan
Phaeodactylum tricornutum go.ptri.csv.gz (46.53 MB) interpro.ptri.csv.gz (972.42 KB) mapman.ptri.csv.gz (309.00 B)
Thalassiosira pseudonana go.tps.csv.gz (44.93 MB) interpro.tps.csv.gz (954.60 KB) mapman.tps.csv.gz (307.00 B)
Thalassiosira oceanica go.tho.csv.gz (47.82 MB) interpro.tho.csv.gz (1.25 MB) mapman.tho.csv.gz (325.00 B)
Pseudo-nitzschia multiseries go.psm.csv.gz (45.72 MB) interpro.psm.csv.gz (1011.86 KB) mapman.psm.csv.gz (291.00 B)
Fistulifera solaris go.fso.csv.gz (84.59 MB) interpro.fso.csv.gz (1.74 MB) mapman.fso.csv.gz (287.00 B)
Fragilariopsis cylindrus go.fcy.csv.gz (53.07 MB) interpro.fcy.csv.gz (1.18 MB) mapman.fcy.csv.gz (310.00 B)
Cyclotella cryptica go.cycr.csv.gz (51.16 MB) interpro.cycr.csv.gz (1.19 MB) mapman.cycr.csv.gz (288.00 B)
Aureococcus anophagefferens go.aan.csv.gz (48.04 MB) interpro.aan.csv.gz (1.18 MB) mapman.aan.csv.gz (297.00 B)
Ectocarpus siliculosus go.esi.csv.gz (46.79 MB) interpro.esi.csv.gz (1.24 MB) mapman.esi.csv.gz (287.00 B)
Nannochloropsis gaditana go.nga.csv.gz (37.96 MB) interpro.nga.csv.gz (806.29 KB) mapman.nga.csv.gz (325.00 B)
Homo sapiens go.hom.csv.gz (166.65 MB) interpro.hom.csv.gz (3.00 MB) mapman.hom.csv.gz (287.00 B)
Drosophila melanogaster go.drm.csv.gz (74.03 MB) interpro.drm.csv.gz (1.67 MB) mapman.drm.csv.gz (294.00 B)
Caenorhabditis elegans go.cel.csv.gz (75.98 MB) interpro.cel.csv.gz (1.38 MB) mapman.cel.csv.gz (294.00 B)
Saccharomyces cerevisiae strain S288C go.sac.csv.gz (43.45 MB) interpro.sac.csv.gz (546.42 KB) mapman.sac.csv.gz (303.00 B)
Schizosaccharomyces pombe go.scp.csv.gz (38.00 MB) interpro.scp.csv.gz (497.67 KB) mapman.scp.csv.gz (309.00 B)
Arabidopsis thaliana go.ath.csv.gz (121.63 MB) interpro.ath.csv.gz (3.52 MB) mapman.ath.csv.gz (267.00 B)
Cyanidioschyzon merolae go.cme.csv.gz (30.41 MB) interpro.cme.csv.gz (470.09 KB) mapman.cme.csv.gz (282.00 B)
Chondrus crispus go.ccr.csv.gz (36.45 MB) interpro.ccr.csv.gz (631.75 KB) mapman.ccr.csv.gz (318.00 B)
Galdieria sulphuraria go.gsu.csv.gz (41.69 MB) interpro.gsu.csv.gz (631.72 KB) mapman.gsu.csv.gz (324.00 B)
Emiliania huxleyi go.emh.csv.gz (86.88 MB) interpro.emh.csv.gz (1.49 MB) mapman.emh.csv.gz (303.00 B)
Paramecium tetraurelia go.pte.csv.gz (165.55 MB) interpro.pte.csv.gz (1.64 MB) mapman.pte.csv.gz (302.00 B)
Seminavis robusta go.sro.csv.gz (67.55 MB) interpro.sro.csv.gz (2.06 MB) mapman.sro.csv.gz (262.00 B)
Synedra acus go.sya.csv.gz (69.43 MB) interpro.sya.csv.gz (1.66 MB) mapman.sya.csv.gz (308.00 B)
Physcomitrella patens go.ppa.csv.gz (116.87 MB) interpro.ppa.csv.gz (2.38 MB) mapman.ppa.csv.gz (300.00 B)
Chlamydomonas reinhardtii go.cre.csv.gz (54.57 MB) interpro.cre.csv.gz (1.32 MB) mapman.cre.csv.gz (303.00 B)
Pseudo-nitzschia multistriata go.pmu.csv.gz (43.07 MB) interpro.pmu.csv.gz (896.33 KB) mapman.pmu.csv.gz (316.00 B)

These files contain sequences for each locus/transcript for each of the organisms in this PLAZA instance.

  • CDS: Coding Sequences. The concatenated exonic DNA sequence per locus/transcript (coding genes only), from start codon to stop codon.
  • Transcript: Transcript sequences. The spliced transcribed DNA sequence per locus/transcript (all gene types). Contains UTR regions.
  • Protein: Amino Acid Sequences. The translated coding sequence per gene, using the appropriate translation table
SpeciesCDS filesTranscript filesProtein files
All transcriptsSelected transcriptAll transcriptsSelected transcriptAll transcriptsSelected transcript
Phaeodactylum tricornutum File 1 (5.12 MB) File 2 (5.12 MB) File 3 (5.14 MB) File 4 (63.00 B) File 5 (3.43 MB) File 6 (3.43 MB)
Thalassiosira pseudonana File 1 (4.92 MB) File 2 (4.92 MB) File 3 (4.89 MB) File 4 (62.00 B) File 5 (3.32 MB) File 6 (3.32 MB)
Thalassiosira oceanica File 1 (10.49 MB) File 2 (10.49 MB) File 3 (10.56 MB) File 4 (957.64 KB) File 5 (7.05 MB) File 6 (7.05 MB)
Pseudo-nitzschia multiseries File 1 (6.33 MB) File 2 (6.33 MB) File 3 (6.77 MB) File 4 (6.77 MB) File 5 (4.28 MB) File 6 (4.28 MB)
Fistulifera solaris File 1 (8.65 MB) File 2 (8.64 MB) File 3 (11.71 MB) File 4 (11.71 MB) File 5 (5.82 MB) File 6 (5.82 MB)
Fragilariopsis cylindrus File 1 (7.35 MB) File 2 (7.35 MB) File 3 (7.74 MB) File 4 (62.00 B) File 5 (4.99 MB) File 6 (4.99 MB)
Cyclotella cryptica File 1 (7.99 MB) File 2 (7.99 MB) File 3 (8.02 MB) File 4 (8.02 MB) File 5 (5.39 MB) File 6 (5.39 MB)
Aureococcus anophagefferens File 1 (4.73 MB) File 2 (4.73 MB) File 3 (58.00 B) File 4 (4.84 MB) File 5 (3.29 MB) File 6 (3.29 MB)
Ectocarpus siliculosus File 1 (7.27 MB) File 2 (7.27 MB) File 3 (13.22 MB) File 4 (62.00 B) File 5 (4.82 MB) File 6 (4.82 MB)
Nannochloropsis gaditana File 1 (3.85 MB) File 2 (3.67 MB) File 3 (3.82 MB) File 4 (3.65 MB) File 5 (2.55 MB) File 6 (2.45 MB)
Homo sapiens File 1 (20.04 MB) File 2 (10.48 MB) File 3 (41.15 MB) File 4 (20.35 MB) File 5 (12.98 MB) File 6 (6.92 MB)
Drosophila melanogaster File 1 (11.00 MB) File 2 (6.28 MB) File 3 (11.85 MB) File 4 (7.00 MB) File 5 (6.85 MB) File 6 (4.08 MB)
Caenorhabditis elegans File 1 (9.53 MB) File 2 (7.09 MB) File 3 (10.69 MB) File 4 (8.15 MB) File 5 (6.35 MB) File 6 (4.78 MB)
Saccharomyces cerevisiae strain S288C File 1 (2.48 MB) File 2 (2.48 MB) File 3 (2.49 MB) File 4 (62.00 B) File 5 (1.67 MB) File 6 (1.67 MB)
Schizosaccharomyces pombe File 1 (2.04 MB) File 2 (2.04 MB) File 3 (2.61 MB) File 4 (62.00 B) File 5 (1.38 MB) File 6 (1.38 MB)
Arabidopsis thaliana File 1 (11.55 MB) File 2 (9.32 MB) File 3 (17.21 MB) File 4 (14.20 MB) File 5 (7.75 MB) File 6 (6.26 MB)
Cyanidioschyzon merolae File 1 (2.14 MB) File 2 (2.14 MB) File 3 (2.18 MB) File 4 (2.18 MB) File 5 (1.42 MB) File 6 (1.42 MB)
Chondrus crispus File 1 (2.94 MB) File 2 (2.90 MB) File 3 (2.90 MB) File 4 (2.86 MB) File 5 (1.95 MB) File 6 (1.95 MB)
Galdieria sulphuraria File 1 (2.43 MB) File 2 (2.40 MB) File 3 (2.40 MB) File 4 (2.37 MB) File 5 (1.62 MB) File 6 (1.62 MB)
Emiliania huxleyi File 1 (10.73 MB) File 2 (10.73 MB) File 3 (10.79 MB) File 4 (682.01 KB) File 5 (7.20 MB) File 6 (7.20 MB)
Paramecium tetraurelia File 1 (14.87 MB) File 2 (14.87 MB) File 3 (14.89 MB) File 4 (9.30 MB) File 5 (10.21 MB) File 6 (10.21 MB)
Seminavis robusta File 1 (15.14 MB) File 2 (14.71 MB) File 3 (17.51 MB) File 4 (62.00 B) File 5 (10.23 MB) File 6 (9.93 MB)
Synedra acus File 1 (9.27 MB) File 2 (9.25 MB) File 3 (9.29 MB) File 4 (9.27 MB) File 5 (6.20 MB) File 6 (6.18 MB)
Physcomitrella patens File 1 (19.83 MB) File 2 (10.08 MB) File 3 (35.09 MB) File 4 (18.40 MB) File 5 (13.17 MB) File 6 (6.79 MB)
Chlamydomonas reinhardtii File 1 (11.14 MB) File 2 (10.19 MB) File 3 (16.89 MB) File 4 (15.45 MB) File 5 (7.34 MB) File 6 (6.71 MB)
Pseudo-nitzschia multistriata File 1 (5.54 MB) File 2 (5.49 MB) File 3 (7.15 MB) File 4 (7.09 MB) File 5 (3.71 MB) File 6 (3.68 MB)

These files contain the information about genes that are detected as being duplicates due to a segmental duplication event or a whole genome duplication event, for all the species within this PLAZA instance.

The files contain gene-pairs (i.e. the duplicates), as well as the associated Ks value (#of synonymous substitutions per synonymous site).
SpeciesAnchorpoints
Phaeodactylum tricornutum Not Available
Thalassiosira pseudonana Not Available
Thalassiosira oceanica Not Available
Pseudo-nitzschia multiseries Not Available
Fistulifera solaris Not Available
Fragilariopsis cylindrus Not Available
Cyclotella cryptica Not Available
Aureococcus anophagefferens Not Available
Ectocarpus siliculosus Not Available
Nannochloropsis gaditana Not Available
Homo sapiens Not Available
Drosophila melanogaster Not Available
Caenorhabditis elegans Not Available
Saccharomyces cerevisiae strain S288C Not Available
Schizosaccharomyces pombe Not Available
Arabidopsis thaliana Not Available
Cyanidioschyzon merolae Not Available
Chondrus crispus Not Available
Galdieria sulphuraria Not Available
Emiliania huxleyi Not Available
Paramecium tetraurelia Not Available
Seminavis robusta Not Available
Synedra acus Not Available
Physcomitrella patens Not Available
Chlamydomonas reinhardtii Not Available
Pseudo-nitzschia multistriata Not Available

These files contain the gene family information for the (coding) genes within this PLAZA instance, separated per gene family type

The following data files are available:
  • Gene family - gene mapping: mapping between the gene families and their constituent genes. Each gene can be part of only 1 gene family (per family type).
  • Gene family functional annotation: the functional annotation per gene family (GO/InterPro), which is based on enrichment analysis of the constituent genes in the family.Also included is a global score which reflects both the enrichment score and the associated p-value.See the documentation for more information.
Data TypeHomologous gene familyOrthologous gene family
Homologous gene family genefamily_data.HOMFAM.csv.gz (3.06 MB) Not Available
Orthologous gene family genefamily_data.ORTHOFAM.csv.gz (2.97 MB) Not Available

These files contain the orthologous relationships between genes, as detected by the various methods within the Integrative Orthology approach.

For more information about the integrative orthology, see the documentation
Orthology TypeData File
Tree-based ortholog integrative_orthology.TROG.csv.gz (39.98 MB)
Orthologous gene family integrative_orthology.ORTHO.csv.gz (244.48 MB)
Anchor point integrative_orthology.anchor_point.csv.gz (1.30 MB)
Best-Hits-and-Inparalogs(BHI)family integrative_orthology.BHIF.csv.gz (70.44 MB)