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Data

This page lists all data sources loaded along with the date the data was downloaded and related publication. NOTE: All external links open in a new window.

Data Category Organism Data Source PubMed Link

Genes

B. taurus

C. hircus

O. aries

NCBI Genes (RefSeq) NCBI Annotation Release 105

Pruitt et al - PubMed 24259432

NCBI FTP
B. taurus Official Gene Set v2.0 Bovine Genome Database

Bovine Genome Sequencing and Analysis Consortium - PubMed 19390049

Reese et al - PubMed 21092105

BGD Download

B. taurus

O. aries

Ensembl Genes Ensembl Release 84 Cunningham et al - PubMed 25352552 Ensembl Download

Homology

B. taurus

C. canis familiaris

E. caballus

H. sapiens

M. musculus

R. norvegicus

S. scrofa

C. hircus

O. aries

Homologous relationships OrthoDB - Version 9 Kriventseva et al - PubMed 25428351 OrthoDB Download

B. taurus

C. canis familiaris

E. caballus

H. sapiens

M. musculus

R. norvegicus

S. scrofa

O. aries

Homologous relationships Treefam - release 8.0 Schreiber et al - PubMed 24194607 EBI FTP

B. taurus

C. canis familiaris

E. caballus

H. sapiens

M. musculus

R. norvegicus

S. scrofa

O. aries

Homologous relationships Ensembl Compara Vilella et al - PubMed 19029536 Ensembl BioMart

B. taurus

C. canis familiaris

H. sapiens

M. musculus

R. norvegicus

S. scrofa

O. aries

Homologous relationships HomoloGene build 68 NCBI Resource Coordinators - PubMed 25398906 NCBI FTP

Proteins

H. sapiens

M. musculus

R. norvegicus

B. taurus

C. hircus

O. aries

Protein annotation UniProt - Release 2016_12 UniProt Consortium - PubMed 25348405 UniProt FTP

H. sapiens

M. musculus

R. norvegicus

B. taurus

C. hircus

O. aries

Protein domains InterPro Version 60 Mitchell et al - PubMed 25428371 InterPro FTP

Interactions

B. taurus

H. sapiens

M. musculus

R. norvegicus

C. hircus

Interactions BioGRID - Version 3.4.144 Chatr-Aryamontri et al - PubMed 25428363 BioGRID Download

H. sapiens

M. musculus

R. norvegicus

B. taurus

O. aries

Interactions IntAct Release 203 Hermjakob H et al - PubMed 14681455 IntAct FTP

Gene Ontology

B. taurus

H. sapiens

M. musculus

R. norvegicus

C. hircus

O. aries

GO annotations GOA at UniProt (GOC Validation Date: 12/16/2016)

Huntley et al - PubMed 25378336

Gene Ontology Consortium - PubMed 25428369

GO Consortium Annotation Download

Pathways

H. sapiens

M. musculus

B. taurus

R. norvegicus

Pathway information inferred through orthologues from curated human pathways Reactome - version 59, Dec 2016 Croft et al - PubMed 24243840 Reactome Download

B. taurus

H. sapiens

M. musculus

Pathway information BioCyc - Version 19.5 Caspi et al - PubMed 26527732 BioCyc

S. scrofa

H. sapiens

M. musculus

B. taurus

R. norvegicus

C. canis familiaris

E. caballus

Pathway information KEGG Kanehisa M et al - PubMed 10592173 KEGG

Publications

B. taurus A mapping from genes to publications NCBI PubMed NCBI Resource Coordinators - PubMed 25398906 NCBI FTP

Variation

B. taurus QTL data for Bos taurus AnimalQTLdb release 30 (Dec 2016) Hu et al - PubMed 17135205 CattleQTLdb Download
B. taurus dbSNP data for Bos taurus dbSNP v146 Sherry et al - PubMed 11125122

NCBI FTP

*SNP arrays and SNP NCBI IDs*

B. taurus SNP Alias Identifiers SNPchiMp v.3 Nicolazzi et al - PubMed 25881165

SNPchiMp

B. taurus dbVar data for Bos taurus dbVar (Revision January, 2016) Church et al - PubMed 23193291 NCBI FTP
B. taurus HapMap data for Bos taurus Bovine HapMap Bovine HapMap Consortium - PubMed 19390050

Variant Annotations

B. taurus Variant effects predicted on RefSeq and Ensembl using Ensembl Variant Effect Predictor Bovine Genome Database

Gene expression

B. taurus

RNA-seq gene expression data from L1 Dominette 01449 and her relatives NCBI SRA Kodama et al - PubMed 22009675 NCBI SRA Project Page

Assembly

B. taurus Chromosome Assembly UMD3.1.1 Zimin et al - PubMed 19393038 NCBI FTP
C. hircus Chromosome Assembly ARS1 Bickhart et al - PubMed 28263316 NCBI FTP
O. aries Chromosome Assembly Oar_v3.1 Jiang et al - PubMed 24904168 NCBI FTP