Data Sources and Species

Release v3.1.0

Data sources

• Core features:

  • Ensembl 75 (Feb 2014) core data is imported for all species.
  • UniProt (release Jan 2015)

• Variation:

  • Ensembl Variation (dbSNP 138)
  • Cosmic
  • Projects: 1000 genomes project, ESP, ExAC
  • HGMD-PUBLIC
  • Poluphen2/Sift

• Regulatory: Human and mouse

  • Ensembl 75 Regulatory build
  • miRNAs:
    • miRBase (release 20)
    • miRTarBase (release 4.5)
    • TargetScan (release 6.0)

• Conservation scores:

  • PhastCons
  • PhyloP

• Clinical association:

  • ClinVar
  • GWAS Catalog
  • COSMIC

• Systems biology:

  • IntAct (release Jan 2014)
  • Reactome 51

• Others:

  • Gene Expression Atlas
  • Gene disease association: DisGeNET

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