Expansion_plot
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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.
Additionally, extra information such as naming conventions, source information, version information, publication information, etc. are also provided.
| Species | Data File |
|---|---|
| All Species | species_information.csv.gz (2.10 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.
This includes gene identifier information, coordinate information, strand information, etc.
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.
This includes gene identifier information, coordinate information, strand information, etc.
| Species | All transcripts | Selected transcript | ||
|---|---|---|---|---|
| All features | Exon features only | All features | Exon features only | |
| Amborella trichopoda | File 1 (3.67 MB) | File 2 (2.57 MB) | File 3 (3.67 MB) | File 4 (2.57 MB) |
| Arabidopsis thaliana | File 1 (4.06 MB) | File 2 (2.62 MB) | File 3 (4.06 MB) | File 4 (2.62 MB) |
| Asterochloris sp. Cgr-DA1pho v2.0 | File 1 (1.99 MB) | File 2 (1.44 MB) | File 3 (1.99 MB) | File 4 (1.44 MB) |
| Aureococcus anophagefferens | File 1 (1020.67 KB) | File 2 (751.89 KB) | File 3 (1020.75 KB) | File 4 (752.06 KB) |
| Auxenochlorella protothecoides | File 1 (956.46 KB) | File 2 (707.38 KB) | File 3 (956.46 KB) | File 4 (707.38 KB) |
| Bathycoccus prasinos | File 1 (427.10 KB) | File 2 (325.50 KB) | File 3 (427.09 KB) | File 4 (325.51 KB) |
| Caenorhabditis elegans | File 1 (5.11 MB) | File 2 (3.98 MB) | File 3 (3.94 MB) | File 4 (3.26 MB) |
| Chlamydomonas reinhardtii | File 1 (4.23 MB) | File 2 (3.02 MB) | File 3 (4.23 MB) | File 4 (3.02 MB) |
| Chlorella sp NC64A | File 1 (1.87 MB) | File 2 (1.32 MB) | File 3 (1.87 MB) | File 4 (1.32 MB) |
| Chondrus crispus | File 1 (641.73 KB) | File 2 (516.78 KB) | File 3 (642.02 KB) | File 4 (516.93 KB) |
| Coccomyxa subellipsoidea C-169 | File 1 (1.94 MB) | File 2 (1.41 MB) | File 3 (1.94 MB) | File 4 (1.41 MB) |
| Cyanidioschyzon merolae | File 1 (253.61 KB) | File 2 (207.49 KB) | File 3 (253.61 KB) | File 4 (207.49 KB) |
| Dictyostelium discoideum | File 1 (1.16 MB) | File 2 (951.41 KB) | File 3 (1.16 MB) | File 4 (950.75 KB) |
| Drosophila melanogaster | File 1 (3.38 MB) | File 2 (2.47 MB) | File 3 (1.86 MB) | File 4 (1.51 MB) |
| Ectocarpus siliculosus | File 1 (3.09 MB) | File 2 (2.18 MB) | File 3 (3.09 MB) | File 4 (2.18 MB) |
| Emiliania huxleyi | File 1 (4.04 MB) | File 2 (3.12 MB) | File 3 (4.04 MB) | File 4 (3.12 MB) |
| Fragilariopsis cylindrus | File 1 (1.51 MB) | File 2 (1.08 MB) | File 3 (1.51 MB) | File 4 (1.08 MB) |
| Galdieria sulphuraria | File 1 (689.20 KB) | File 2 (527.87 KB) | File 3 (689.41 KB) | File 4 (527.92 KB) |
| Helicosporidium sp. | File 1 (479.30 KB) | File 2 (363.88 KB) | File 3 (479.30 KB) | File 4 (363.88 KB) |
| Homo sapiens | File 1 (20.79 MB) | File 2 (16.13 MB) | File 3 (7.36 MB) | File 4 (6.35 MB) |
| Micromonas pusilla strain CCMP1545 | File 1 (685.00 KB) | File 2 (529.72 KB) | File 3 (685.02 KB) | File 4 (529.73 KB) |
| Micromonas sp RCC299 | File 1 (783.02 KB) | File 2 (546.07 KB) | File 3 (782.90 KB) | File 4 (546.01 KB) |
| Mus musculus | File 1 (12.45 MB) | File 2 (9.54 MB) | File 3 (5.83 MB) | File 4 (4.84 MB) |
| Nannochloropsis gaditana | File 1 (941.63 KB) | File 2 (728.67 KB) | File 3 (915.29 KB) | File 4 (712.34 KB) |
| Oryza sativa | File 1 (5.60 MB) | File 2 (4.03 MB) | File 3 (5.60 MB) | File 4 (4.03 MB) |
| Ostreococcus lucimarinus | File 1 (473.22 KB) | File 2 (341.02 KB) | File 3 (473.23 KB) | File 4 (341.02 KB) |
| Ostreococcus mediterraneus | File 1 (442.35 KB) | File 2 (342.44 KB) | File 3 (442.35 KB) | File 4 (342.45 KB) |
| Ostreococcus sp RCC809 | File 1 (505.16 KB) | File 2 (379.82 KB) | File 3 (505.23 KB) | File 4 (379.70 KB) |
| Ostreococcus tauri | File 1 (433.17 KB) | File 2 (331.52 KB) | File 3 (433.18 KB) | File 4 (331.53 KB) |
| Paramecium tetraurelia | File 1 (3.93 MB) | File 2 (3.03 MB) | File 3 (3.93 MB) | File 4 (3.03 MB) |
| Phaeodactylum tricornutum | File 1 (786.27 KB) | File 2 (563.62 KB) | File 3 (786.27 KB) | File 4 (563.62 KB) |
| Physcomitrella patens | File 1 (4.84 MB) | File 2 (3.51 MB) | File 3 (4.84 MB) | File 4 (3.51 MB) |
| Phytophtora sojae | File 1 (1.66 MB) | File 2 (1.29 MB) | File 3 (1.66 MB) | File 4 (1.29 MB) |
| Picochlorum sp. SENEW3 (SE3) | File 1 (481.27 KB) | File 2 (368.35 KB) | File 3 (481.28 KB) | File 4 (368.35 KB) |
| Picochlorum_RCC4223 | File 1 (590.15 KB) | File 2 (436.78 KB) | File 3 (590.15 KB) | File 4 (436.79 KB) |
| Saccharomyces cerevisiae strain S288C | File 1 (363.03 KB) | File 2 (301.95 KB) | File 3 (362.94 KB) | File 4 (301.99 KB) |
| Schizosaccharomyces pombe | File 1 (477.23 KB) | File 2 (389.13 KB) | File 3 (477.17 KB) | File 4 (389.11 KB) |
| Thalassiosira pseudonana | File 1 (1.07 MB) | File 2 (796.33 KB) | File 3 (1.07 MB) | File 4 (796.29 KB) |
| Volvox carteri | File 1 (2.75 MB) | File 2 (2.02 MB) | File 3 (2.75 MB) | File 4 (2.02 MB) |
These files contain the mapping between genes and transcripts.
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.
Many genes are known by their aliases (e.g. E2F3 for AT2G36010). These files contain this kind of identifier mappings.
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:
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:
- More information about Gene Ontology: http://www.geneontology.org/
- More information about InterPro: https://www.ebi.ac.uk/interpro/
- More information about MapMan: https://mapman.gabipd.org/
These files contain the genomic sequences for each of the organisms present in this PLAZA instance.
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
| Species | CDS files | Transcript files | Protein files | |||
|---|---|---|---|---|---|---|
| All transcripts | Selected transcript | All transcripts | Selected transcript | All transcripts | Selected transcript | |
| Amborella trichopoda | File 1 (7.19 MB) | File 2 (7.19 MB) | Not Available | Not Available | File 5 (4.82 MB) | File 6 (4.82 MB) |
| Arabidopsis thaliana | File 1 (9.32 MB) | File 2 (9.32 MB) | Not Available | Not Available | File 5 (6.26 MB) | File 6 (6.26 MB) |
| Asterochloris sp. Cgr-DA1pho v2.0 | File 1 (3.63 MB) | File 2 (3.63 MB) | Not Available | Not Available | File 5 (2.49 MB) | File 6 (2.49 MB) |
| Aureococcus anophagefferens | File 1 (4.73 MB) | File 2 (4.73 MB) | Not Available | Not Available | File 5 (3.29 MB) | File 6 (3.29 MB) |
| Auxenochlorella protothecoides | File 1 (2.24 MB) | File 2 (2.24 MB) | Not Available | Not Available | File 5 (1.53 MB) | File 6 (1.53 MB) |
| Bathycoccus prasinos | File 1 (3.44 MB) | File 2 (3.44 MB) | Not Available | Not Available | File 5 (2.33 MB) | File 6 (2.33 MB) |
| Caenorhabditis elegans | File 1 (9.50 MB) | File 2 (7.02 MB) | Not Available | Not Available | File 5 (6.28 MB) | File 6 (4.73 MB) |
| Chlamydomonas reinhardtii | File 1 (10.16 MB) | File 2 (10.16 MB) | Not Available | Not Available | File 5 (6.69 MB) | File 6 (6.69 MB) |
| Chlorella sp NC64A | File 1 (3.54 MB) | File 2 (3.54 MB) | Not Available | Not Available | File 5 (2.43 MB) | File 6 (2.43 MB) |
| Chondrus crispus | File 1 (2.90 MB) | File 2 (2.90 MB) | Not Available | Not Available | File 5 (1.95 MB) | File 6 (1.95 MB) |
| Coccomyxa subellipsoidea C-169 | File 1 (3.45 MB) | File 2 (3.45 MB) | Not Available | Not Available | File 5 (2.34 MB) | File 6 (2.34 MB) |
| Cyanidioschyzon merolae | File 1 (2.14 MB) | File 2 (2.14 MB) | Not Available | Not Available | File 5 (1.43 MB) | File 6 (1.43 MB) |
| Dictyostelium discoideum | File 1 (5.43 MB) | File 2 (5.42 MB) | Not Available | Not Available | File 5 (3.74 MB) | File 6 (3.73 MB) |
| Drosophila melanogaster | File 1 (10.85 MB) | File 2 (6.28 MB) | Not Available | Not Available | File 5 (6.82 MB) | File 6 (4.08 MB) |
| Ectocarpus siliculosus | File 1 (7.09 MB) | File 2 (7.09 MB) | Not Available | Not Available | File 5 (4.69 MB) | File 6 (4.69 MB) |
| Emiliania huxleyi | File 1 (10.73 MB) | File 2 (10.73 MB) | Not Available | Not Available | File 5 (7.20 MB) | File 6 (7.20 MB) |
| Fragilariopsis cylindrus | File 1 (6.28 MB) | File 2 (6.28 MB) | Not Available | Not Available | File 5 (4.25 MB) | File 6 (4.25 MB) |
| Galdieria sulphuraria | File 1 (2.38 MB) | File 2 (2.38 MB) | Not Available | Not Available | File 5 (1.61 MB) | File 6 (1.61 MB) |
| Helicosporidium sp. | File 1 (1.40 MB) | File 2 (1.40 MB) | Not Available | Not Available | File 5 (977.77 KB) | File 6 (977.77 KB) |
| Homo sapiens | File 1 (18.43 MB) | File 2 (8.36 MB) | Not Available | Not Available | File 5 (10.13 MB) | File 6 (5.51 MB) |
| Micromonas pusilla strain CCMP1545 | File 1 (4.31 MB) | File 2 (4.31 MB) | Not Available | Not Available | File 5 (2.98 MB) | File 6 (2.98 MB) |
| Micromonas sp RCC299 | File 1 (4.04 MB) | File 2 (4.04 MB) | Not Available | Not Available | File 5 (2.76 MB) | File 6 (2.76 MB) |
| Mus musculus | File 1 (14.53 MB) | File 2 (7.87 MB) | Not Available | Not Available | File 5 (7.85 MB) | File 6 (5.22 MB) |
| Nannochloropsis gaditana | File 1 (3.81 MB) | File 2 (3.67 MB) | Not Available | Not Available | File 5 (2.55 MB) | File 6 (2.45 MB) |
| Oryza sativa | File 1 (11.93 MB) | File 2 (11.93 MB) | Not Available | Not Available | File 5 (8.00 MB) | File 6 (8.00 MB) |
| Ostreococcus lucimarinus | File 1 (2.60 MB) | File 2 (2.60 MB) | Not Available | Not Available | File 5 (1.76 MB) | File 6 (1.76 MB) |
| Ostreococcus mediterraneus | File 1 (3.09 MB) | File 2 (3.09 MB) | Not Available | Not Available | File 5 (2.09 MB) | File 6 (2.09 MB) |
| Ostreococcus sp RCC809 | File 1 (2.67 MB) | File 2 (2.67 MB) | Not Available | Not Available | File 5 (1.82 MB) | File 6 (1.82 MB) |
| Ostreococcus tauri | File 1 (2.98 MB) | File 2 (2.98 MB) | Not Available | Not Available | File 5 (2.01 MB) | File 6 (2.01 MB) |
| Paramecium tetraurelia | File 1 (14.87 MB) | File 2 (14.87 MB) | Not Available | Not Available | File 5 (10.37 MB) | File 6 (10.37 MB) |
| Phaeodactylum tricornutum | File 1 (5.10 MB) | File 2 (5.10 MB) | Not Available | Not Available | File 5 (3.42 MB) | File 6 (3.42 MB) |
| Physcomitrella patens | File 1 (9.72 MB) | File 2 (9.72 MB) | Not Available | Not Available | File 5 (6.56 MB) | File 6 (6.56 MB) |
| Phytophtora sojae | File 1 (7.73 MB) | File 2 (7.73 MB) | Not Available | Not Available | File 5 (5.12 MB) | File 6 (5.12 MB) |
| Picochlorum sp. SENEW3 (SE3) | File 1 (2.76 MB) | File 2 (2.76 MB) | Not Available | Not Available | File 5 (1.87 MB) | File 6 (1.87 MB) |
| Picochlorum_RCC4223 | File 1 (3.30 MB) | File 2 (3.30 MB) | Not Available | Not Available | File 5 (2.22 MB) | File 6 (2.22 MB) |
| Saccharomyces cerevisiae strain S288C | File 1 (2.48 MB) | File 2 (2.48 MB) | Not Available | Not Available | File 5 (1.67 MB) | File 6 (1.67 MB) |
| Schizosaccharomyces pombe | File 1 (2.04 MB) | File 2 (2.04 MB) | Not Available | Not Available | File 5 (1.38 MB) | File 6 (1.38 MB) |
| Thalassiosira pseudonana | File 1 (4.82 MB) | File 2 (4.82 MB) | Not Available | Not Available | File 5 (3.13 MB) | File 6 (3.13 MB) |
| Volvox carteri | File 1 (6.51 MB) | File 2 (6.51 MB) | Not Available | Not Available | File 5 (4.31 MB) | File 6 (4.31 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).
The files contain gene-pairs (i.e. the duplicates), as well as the associated Ks value (#of synonymous substitutions per synonymous site).
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:
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 Type | Gene Family Clusters | Gene Family Enrichments |
|---|---|---|
| Homologous gene family | genefamily_data.HOMFAM.csv.gz (3.34 MB) | Not Available |
| Orthologous gene family | genefamily_data.ORTHOFAM.csv.gz (3.69 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
For more information about the integrative orthology, see the documentation
| Orthology Type | Data File |
|---|---|
| Tree-based ortholog | Not Available |
| Orthologous gene family | integrative_orthology.ORTHO.csv.gz (56.57 MB) |
| Anchor point | integrative_orthology.anchor_point.csv.gz (368.90 KB) |
| Best-Hits-and-Inparalogs(BHI)family | integrative_orthology.BHIF.csv.gz (100.55 MB) |