The source of gene annotations in FAANGMine are NCBI (RefSeq) and Ensembl.
Query for genes:
Quick Search
Search FAANGMine. Enter names, identifiers or keywords for genes, proteins, ontology terms, authors, etc. (e.g. RCAN1, COX2, NM_001040473.2, NP_001076063.1, 282087, ENSFCAG00000031270, rs385910977, IL13)
Quick List
Enter a list of identifiers.
First Time Here?
FAANGMine v1.2 (release updates) integrates reference genome assemblies of bovine, goat, horse, pig, sheep, chicken, cat, dog and water buffalo with many other biological data sets. See the Data Source page for assembly versions. Model organism data (human, mouse, rat) allow well-curated data sets to be applied 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 |
FAANG |
Proteins |
Function |
Homology |
Variation |
Entire Gene Set |
Alias and DBXref |
Gene expression values (FPKM and TPM) were computed using RNAseq from gene atlas expression datasets. The Data Source page lists expression datasets available for each species.
Query for expression:
This template category is for data and metadata generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. FAANG data currently includes RNA-seq based gene expression levels for several species (under the Expression tab) and equine histone modification marks. The sequence ontology term used for histone modification marks in FAANGMine is "histone_binding_site".
Query for faang:
- Organism
FAANG Analyses - Organism FAANG ChIP-seq Experiments
- Gene ID Overlapping Histone Modification Marks
- Organism FAANG RNA-seq Experiments
- FAANG Analysis Tissue, BioSample IDs and other metadata
- Histone Modification Mark ID All Overlapping Features
- Pooled BioSample ID Component BioSamples
- Histone Modification Mark ID Location and Metadata
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 UniProt. Pathway datasets are from KEGG and Reactome.
Query for function:
Homologue datasets include Ensembl Compara and OrthoDB.
Query for homology:
Variation data includes variant and variant effects from Ensembl (all species except water buffalo) and QTL from AnimalQTLdb (bovine, pig, sheep, chicken). Primary identifiers for SNP are rs IDs. Identifiers from SNP arrays are available as alias identifiers. You can convert alias IDs to rs IDs using a query template.
Query for variation:
These template queries allow retrieval of an entire dataset for a specified organism or gene set.
Query for entire gene set:
- Gene Source and Organism Gene IDs
- Organism All QTL
- Organism All proteins
- Genome Assembly Chromosome IDs and Lengths
- Gene Source and Organism Genes and Database Cross Reference IDs
- Organism Proteins (UniProt) and Publications.
- Organism Transcripts + Genes + Database Cross Reference IDs
- Gene Source and Organism Genes and Chromosomal location
These template queries enable the retrieval of database cross references (DBxref) and aliases. DBxref are provided for gene ids across different gene sets (RefSeq and Ensembl). Aliases are provided for SNP ids.
Query for alias and dbxref:
This material is based upon work supported by the National Science Foundation under Award Number 0054449. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. FAANGMine is hosted at the University of Missouri.
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