ChemiRs: a web application for microRNAs and chemicals.
BACKGROUND
MicroRNAs (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.


RESULTS
We 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.


CONCLUSIONS
Here, 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 .
Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.
Emily Chia-Yu
EC
Su
Department of Life Science, College of Science, National Taiwan Normal University, Taipei, 116, Taiwan.
Yu-Sing
YS
Chen
Department of Life Science, College of Science, National Taiwan Normal University, Taipei, 116, Taiwan.
Yun-Cheng
YC
Tien
Department of Civil Engineering, College of Engineering, National Taiwan University College of Engineering, Taipei, 106, Taiwan.
Jeff
J
Liu
Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan.
Bing-Ching
BC
Ho
Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan.
Sung-Liang
SL
Yu
Department of Life Science, College of Science, National Taiwan Normal University, Taipei, 116, Taiwan. sher@ntnu.edu.tw.
Sher
S
Singh
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D046650:Medical Subject Headings; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics*; D039781:PubMed; D012984:Software
D035683:MicroRNAs
Chemical; Disease; Gene ontology; Genomics; microRNA