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Data Sources and Species
javild edited this page Nov 17, 2016
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- Ensembl Release 79 (March 2015): Core data for all species are built from Ensembl v79, so Homo sapiens uses now assembly GRCh38.p2 and GENCODE 22, you can query the rest of assemblies at Ensembl table of assemblies. These includes genome sequence, gene sets, variation and regulation. Ensembl Release 75 (Feb 2014) is used only for keeping old Homo sapiens GRCh37 assembly.
- UniProt (Release March 2015)
- InterPro v50 v50 (Release Feb 2015)
- Polyphen2/Sift from Ensembl v79
- Ensembl v79 Variation (dbSNP 142)
- Population frequencies: 1000 genomes project, ESP (ExAC in preparation).
- Ensembl v79 Regulatory
- miRNAs:
- miRBase (Release 21)
- miRTarBase (Release 4.5)
- TargetScan (Release 6.0)
- ClinVar (Release March 2015)
- GWAS Catalog
- COSMIC v71 (Release March 2015)
- PhastCons
- PhyloP
- (GERP++ in preparation)
- IntAct (Release March 2015)
- (Reactome 51 in preparation)
- Gene Expression Atlas
- Gene disease association: DisGeNET
- DGIdb: http://dgidb.genome.wustl.edu/
species |
Name | Scientific name | Assembly |
|---|---|---|---|
| hsapiens | human | Homo sapiens | GRCh37.p13 |
| mmusculus | mouse | Mus musculus | GRCm38.p2 |
| rnorvegicus | rat | Rattus norvegicus | Rnor_5.0 |
| ptroglodytes | chimp | Pan troglodytes | CHIMP2.1.4 |
| ggorilla | gorilla | Gorilla gorilla | gorGor3.1 |
| pabelii | orangutan | Pongo abelii | PPYG2 |
| mmulatta | macaque | Macaca mulatta | MMUL 1.0 |
| sscrofa | pig | Sus scrofa | Sscrofa10.2 |
| cfamiliaris | dog | Canis familiaris | CanFam 3.1 |
| ecaballus | horse | Equus caballus | Equ Cab 2 |
| ocuniculus | rabbit | Oryctolagus cuniculus | OryCun2.0 |
| ggallus | chicken | Gallus gallus | Galgal4 |
| btaurus | cow | Bos taurus | UMD3.1 |
| fcatus | cat | Felis catus | Felis_catus_6.2 |
| drerio | zebrafish | Danio rerio | Zv9 |
| cintestinalis | Ciona intestinalis | KH | |
| dmelanogaster | fruitfly | Drosophila melanogaster | BDGP 5 |
| dsimulans | Drosophila simulans | dsim_caf1 | |
| dyakuba | Drosophila yakuba | dyak_caf1 | |
| agambiae | mosquito | Anopheles gambiae | AgamP4 |
| celegans | worm | Caenorhabditis elegans | WS235 |
| scerevisiae | yeast | Saccharomyces cerevisiae | R64-1-1 |
| spombe | Schizosaccharomyces pombe | ASM294v2 | |
| afumigatus | Aspergillus fumigatus | TIGR | |
| aniger | Aspergillus niger | DSM | |
| anidulans | Aspergillus nidulans | ASM1142v1 | |
| aoryzae | Aspergillus oryzae | NITE | |
| pfalciparum | malaria parasite | Plasmodium falciparum | 3D7 |
| lmajor | Plasmodium falciparum | ASM276v1 | |
| athaliana | Arabidopsis thaliana | TAIR10 | |
| alyrata | Arabidopsis lyrata | v.1.0 | |
| bdistachyon | Brachypodium distachyon | v1.0 | |
| osativa | Oryza sativa Indica | ASM465v1 | |
| gmax | Glycine max | V1.0 | |
| vvinifera | Vitis vinifera | IGGP_12x | |
| zmays | Zea mays | AGPv3 |