Abstract
BackgroundMicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human health. Chemicals in environment affect our health and daily life, and some of them can lead to diseases by inferring biological pathways.ResultsWe develop a creditable online web server, ChemiRs, for predicting interactions and relations among miRNAs, chemicals and pathways. The database not only compares gene lists affected by chemicals and miRNAs, but also incorporates curated pathways to identify possible interactions.ConclusionsHere, we manually retrieved associations of miRNAs and chemicals from biomedical literature. We developed an online system, ChemiRs, which contains miRNAs, diseases, Medical Subject Heading (MeSH) terms, chemicals, genes, pathways and PubMed IDs. We connected each miRNA to miRBase, and every current gene symbol to HUGO Gene Nomenclature Committee (HGNC) for genome annotation. Human pathway information is also provided from KEGG and REACTOME databases. Information about Gene Ontology (GO) is queried from GO Online SQL Environment (GOOSE). With a user-friendly interface, the web application is easy to use. Multiple query results can be easily integrated and exported as report documents in PDF format. Association analysis of miRNAs and chemicals can help us understand the pathogenesis of chemical components. ChemiRs is freely available for public use at http://omics.biol.ntnu.edu.tw/ChemiRs.
Highlights
MicroRNAs are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human
Su et al BMC Bioinformatics (2016) 17:167 study, we develop a ChemiRs web server, in which various miRNA prediction methods and biological databases are integrated and relations between miRNAs, chemicals, genes, diseases and pathways are analyzed
We manually retrieved the associations of miRNAs and chemicals from biomedical literature, and downloaded toxicogenomics data from the comparative toxicogenomic database (CTD; http://ctd.mdibl.org) [10]
Summary
We develop a creditable online web server, ChemiRs, for predicting interactions and relations among miRNAs, chemicals and pathways. The database compares gene lists affected by chemicals and miRNAs, and incorporates curated pathways to identify possible interactions
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