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 | *SNP arrays and SNP NCBI IDs* |
|
| B. taurus | SNP Alias Identifiers | SNPchiMp v.3 | Nicolazzi et al - PubMed 25881165 | ||
| 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 | |
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