Gene models in HymenopteraMine come from multiple sources including NCBI RefSeq and consortium official gene sets. RefSeq data sources are labeled with 4-letter species code and "_RefSeq" in pull down menus. Consortium data sources are labeled using the original consortium official gene set names, and may have "HGD" appended, if the data source has ids assigned by HGD. Use "ALIAS AND DBXREF" templates to convert identifiers.
Query for genes:
HymenopteraMine includes expression values for A. mellifera transcripts computed based on aligned RNAseq reads from the NCBI SRA libraries. Metadata from the SRA is also included. Expression for additional species will be incorporated in future loads.
Query for gene expression:
HymenopteraMine includes protein information from UniProt and protein domain information for UniProt proteins from InterPro. Although UniProt uses protein isoform identifiers as primary identifiers, it maps UniProt ids to RefSeq genes rather than to specific Refseq transcript identifiers. Therefore, HymenopteraMine maps UniProt ids to RefSeq genes. Queries relating RefSeq genes to UniProt may produce multiple results per gene due to the presence of protein isoforms.
Query for protein:
HymenopteraMine includes orthologue predictions from Orthodb, which identifies orthologous groups of genes that are descended from a single ancestral gene. HymenopteraMine uses the OrthoDB data set computed based on common insect ancestors to allow the inclusion of Drosophila melanogaster (a Dipteran). This means that any orthologous group in HymenopteraMine can include duplicated genes that emerged after divergence from the common insect ancestor. All pairwise relationships within an orthologous group are called orthologues even if some might be classified as paralogues in an analysis of a smaller taxonomic group (e.g. the relationship between A. mellifera and A. florea genes since divergence from a single Apis ancestor).
Query for homology:
HymenopteraMine includes GO annotations for most species, KEGG pathways for A. mellifera and D. melanogaster, Reactome and Fly Reactome pathways for D. melanogaster, and interactions (BioGRID and IntAct) for D. melanogaster. You can use orthologous relationships to leverage A. mellifera and D. melanogaster information for other species.
Query for function:
HymenopteraMine includes sequence variants for A. mellifera from dbSNP, as well as variant consequences computed at HGD
Query for variation:
The query templates in this category allow you to perform simple queries on an entire gene or protein set for a species.
Query for entire gene set:
The query templates in this category allow you to convert identifiers. Use a database cross reference query template to convert between a RefSeq and consortium gene set with HGD ids. Use an alias query template to convert between HGD ids and original consortium ids, HGD ids and OrthoDB ids, or HGD ids for old vs new gene sets (e.g. amel_OGSv3.2 vs amel_OGSv1.0). You must use the appropriate alias query template for converting either gene ids or transcript ids, depending on the species. For the following species, aliases are provided for transcripts rather than genes because the original gene sets did not have gene ids: A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Query for alias and dbxref: