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Update in process |
Data sources
Category | Data source | Version/Date | |
---|---|---|---|
CellBase v3 (March 2015) | CellBase v4 (June 2016) | ||
Core | Ensembl Core | v79 | v82 |
Protein | UniProt | March 2015 | |
InterPro | v50 | ||
Polyphen2/Sift | Ensembl 79 | Ensembl 82 | |
Variation | Ensembl Variation | v79 | v82 |
Population Frequencies | |||
Regulatory | Ensembl Regulatory | v79 | v82 |
Conservation | PhastCons | ||
PhyloP | |||
GERP++ | |||
Clinical | ClinVar | March 2015 | |
COSMIC | v71 | ||
HPO | |||
DisGeNET | |||
Biological Networks | Reactome | v51 | |
IntAct | March 2015 | ||
Others | DGIdb | ||
Gene Expression Atlas |
Species
Id | Common Name | Scientific Name | Assembly | |
---|---|---|---|---|
CellBase v3 (March 2015) | CellBase v4 (June 2016) | |||
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 | |
[DEPRECATED] Release v3
Data sources and versions
Core features
- 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**](http://www.ensembl.org/info/website/archives/assembly.html). These includes genome sequence, gene sets, variation and regulation. Ensembl Release 75 (Feb 2014) is used only for keeping old **_Homo sapiens_ GRCh37** assembly.
Protein
- UniProt (Release March 2015)
- InterPro v50 v50 (Release Feb 2015)
- Polyphen2/Sift from Ensembl v79
Variation
- Ensembl v79 Variation (dbSNP 142)
- Population frequencies: 1000 genomes project, ESP (ExAC in preparation).
Regulatory
- Ensembl v79 Regulatory
- miRNAs:
- miRBase (Release 21)
- miRTarBase (Release 4.5)
- TargetScan (Release 6.0)
Clinical association
- ClinVar (Release March 2015)
- GWAS Catalog
- COSMIC v71 (Release March 2015)
Conservation scores
- PhastCons
- PhyloP
- (GERP++ in preparation)
Systems biology
- IntAct (Release March 2015)
- (Reactome 51 in preparation)
Others
- Gene Expression Atlas
- Gene disease association: DisGeNET
- DGIdb: http://dgidb.genome.wustl.edu/
Available species
`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 |
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