Sample information

Chart of sample sizes :

eRNA summary

Animal-eRNAdb identified 242,248 eRNAs from 5085 manual-collecting samples in 10 species including chimpanzee [Pan troglodytes], rhesus [Macaca mulatta],  mouse [Mus musculus], rat [Rattus norvegicus],  sheep [Ovis aries], chicken [Gallus gallus],  frog [Tropical clawed frog], zebrafish [Danio rerio], fly [Drosophila melanogaster], and worm [Caenorhabditis elegans].

Method

flow chart of Animal-eRNAdb

This flow chart contains two parts:
1)  identification of eRNAs: detail information can be viewed at "Identification of eRNAs" in present page;
2) identification of possible regulators of eRNAs, target genes of eRNAs and trait-related eRNAs: detail information is in paper.

identification of eRNAs

This flow chart contains three parts:
1) processing of annotations of enhancers;
2) processing of RNA-seq data;
3) identification of detectable eRNAs.

Function modules

Animal-eRNAdb provides six main modules, including ‘eRNA expression’, ‘trait-related eRNA’, ‘eRNA regulator’, ‘eRNA target gene’, ‘sequence similarity’ and ‘download’, and the users can comprehensively understand one eRNA through different modules. Several search/selection boxes are designed on each page, including species selection box, tissue selection box, trait selection box and eRNA search box. In the eRNA search box, users can query a unique eRNA by entering an eRNA ID, or query all eRNAs located in a certain region by entering the genomic region (A large genomic region needs more time to process data, please be patient or narrow your search region), or query all eRNAs located at ±1 MB around the start site of the selected gene by entering a gene symbol/Ensembl ID.

eRNA expression


At first, users should click "Expression" in navigation bar or animal picture in "Home" page. Then, users can select a species, tissue and enter either an eRNA ID or a genomic region or a gene ID to query eRNA expression. A table with columns of species, bioproject, tissue, eRNA ID, expression and plotAll of the queried eRNAs will be provided. Users can view the eRNA expression across tissues of a given species and the selected tissue is marked as red in the graph by clicking the ‘PlotAll’ button. It's worth mentioning that a large genomic region would take a little more time for data processiong (the same for latter modules).

trait-related eRNA


Users can select a species, tissue, trait and enter either an eRNA ID or a genomic region or a gene ID to query eRNAs associated with the developmental stage and gender in specific tissues of a given species. A table with the columns of species, bioproject, tissue, eRNA ID, trait, FC/F/Rho, FDR and plot of the queried eRNAs will be presented. An association diagram will be shown when clicking ‘Plot’. Users can click the ‘Download’ button to download the queried data or click the ‘?’ button for more information.

eRNA regulator


Users can select a species, tissue and enter either an eRNA ID or a TF ID to search for TFs significantly associated with eRNAs in specific tissues of a given species. Two tables will be shown: one provides the species, tissue, eRNA ID, number of correlated TFs or number of correlated eRNAs and detail, and the other presents the bioproject, tissue, eRNA ID, TF ID, TF symbol, Rho, FDR and plot. Users can view the co-expression correlation diagram between the eRNA and the TF by clicking the ‘Plot’ button.

eRNA target gene


Users can select a species, tissue and enter either an eRNA ID or a gene ID to search for target genes (within 1 MB) that may be regulated by eRNAs in specific tissues of a given species. A table with the columns of species, bioproject, tissue, eRNA ID, gene ID, gene symbol, gene start, gene end, distance, Rho, FDR and detail of the queried eRNAs will be provided, and the correlation diagram between the eRNA and the target gene will be displayed upon the clicking of the ‘Detail’ button.

sequence similarity


Users can select a species and enter either an eRNA ID or a genomic region to browse eRNAs with sequence similarities in multiple species. A table with columns including species, eRNA ID, seq, match species, match eRNA ID, seq, identify and Evalue of the queried eRNAs will be shown. Users can download the sequence of the eRNA by clicking the ‘Seq’ button and download the list of all eRNAs by clicking the ‘Download’ button.

Note

Although Animal-eRNAdb is a valuable resource for understanding the functions and mechanisms of eRNAs across tissues of multiple species, there are still some limitations: the database probably misses many potential eRNAs because only routine RNA-seq data was used and annotations of enhancers were insufficient.