The source of gene annotations in BovineMine are NCBI (RefSeq), Ensembl and the Bovine Genome Database.
Query for genes:
The Keyword search currently has a bug, and we are working to fix it. You can search a gene or protein id by pasting it into the Quick List Box to the right, selecting the correct data type. For data types other than genes or proteins, click "Advanced" under Quick List.
Enter a list of identifiers.
BovineMine v1.6 (release updates) integrates bovine reference genome assemblies (ARS-UCD1.2 and UMD3.1.1) with many other biological data sets, including genomes of other species. The sheep (Oar_v3.1 and Oar_v4.0) and goat (ARS1) genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-curated data sets to be applied to ruminants using orthology.
Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
Genes |
Expression |
Proteins |
Function |
Homology |
Interactions |
Variation |
Entire Gene Set |
Alias and DBXref |
GplusE |
The source of gene annotations in BovineMine are NCBI (RefSeq), Ensembl and the Bovine Genome Database.
Query for genes:
Bovine gene expression values (FPKM and TPM) were computed using RNAseq from Dominette 01449 and her calves and sire.
Query for expression:
Most protein information is from UniProt and InterPro. NCBI (RefSeq) and Ensembl protein ids and sequences are also available.
Query for proteins:
Gene Ontology annotation is from GOA@UniProt and AgBase. Pathway datasets are from KEGG and Reactome. A metabolic reactions dataset computed based on orthology to human RECON2 by the GplusE project is also available.
Query for function:
Homologue datasets include TreeFam, Ensembl Compara and OrthoDB. A new ortholog dataset called ORIS (Orthology inference using synteny) from the GplusE project is also available.
Query for homology:
Interaction datasets include BioGrid and IntAct.
Query for interactions:
Variation datasets include SNP and SNP effects (bovine ARS-UCD1.2 and Ensembl95 genes), SNP id aliases (SNPchiMp) and AnimalQTLdb (bovine ARS-UCD1.2).
Query for variation:
These template queries allow retrieval of an entire dataset for a specified organism or gene set.
Query for entire gene set:
All QTL Gene IDs Transcripts + Genes + Database Cross Reference IDs Genes and Chromosomal location All proteins Genes + mRNA + Protein Chromosome IDs Genes and Database Cross Reference IDsThese template queries enable the retrieval of database cross references (DBxref) and alias. DBxref are provided for gene ids across different gene sets and assemblies. Aliases are provided for SNP ids.
Query for alias and dbxref:
dbSNP rsID SNP Alias IDs Transcripts + Genes + Database Cross Reference IDs Database Cross Reference ID (e.g RefSeq to Ensembl) Genes and Database Cross Reference IDs Database CrossReference ID and Locations Gene ID Database Cross Reference ID and LocationsTemplate queries are provided for datasets generated by the GplusE project, which has been the source of funding for BovineMine development. Current datasets include ORIS (Orthology inference using synteny) and metabolic reactions computed for the ORIS dataset based on RECON2.
Query for gpluse:
Elsik CG, Unni DR, Diesh CM, Tayal A, Emery ML, Nguyen HN, Hagen DE. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res. 2016 Jan 4;44(D1):D834-9. doi: 10.1093/nar/gkv1077. Epub 2015 Oct 19. PubMed PMID: 26481361.
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