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ChemiRs: a web application for microRNAs and chemicals.

Su EC, Chen YS, Tien YC, Liu J, Ho BC, Yu SL, Singh S - BMC Bioinformatics (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.

ABSTRACT

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 .

No MeSH data available.


Related in: MedlinePlus

Query result of ‘DEHP’ by ‘Search by chemical’ module in ChemiRs. Related miRNAs of MeSH ID ‘D004051, Diethylhexyl Phthalate’ are listed
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Fig5: Query result of ‘DEHP’ by ‘Search by chemical’ module in ChemiRs. Related miRNAs of MeSH ID ‘D004051, Diethylhexyl Phthalate’ are listed

Mentions: Here, we exemplify the application of ChemiRs to search by chemicals. We applied ChemiRs to analyze diethylhexyl phthalate (DEHP) by submitting ‘DEHP’ in ‘Search by chemical’ module. After pressing the ‘Refresh’ button, we clicked the Medical Subject Heading (MeSH) ID ‘D004051, Diethylhexyl Phthalate’ and chose ‘None’ as the filter; ‘miRNAs,’ ‘Genes,’ ‘Diseases,’ ‘Pathways,’ and ‘GO terms’ as the output functions; all ten methods as miRNA target prediction methods, and ‘10 minimum predicted methods’ as restrictions, respectively. As shown in Fig. 5, the results can be easily downloaded as CSV files.Fig. 5


ChemiRs: a web application for microRNAs and chemicals.

Su EC, Chen YS, Tien YC, Liu J, Ho BC, Yu SL, Singh S - BMC Bioinformatics (2016)

Query result of ‘DEHP’ by ‘Search by chemical’ module in ChemiRs. Related miRNAs of MeSH ID ‘D004051, Diethylhexyl Phthalate’ are listed
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4836156&req=5

Fig5: Query result of ‘DEHP’ by ‘Search by chemical’ module in ChemiRs. Related miRNAs of MeSH ID ‘D004051, Diethylhexyl Phthalate’ are listed
Mentions: Here, we exemplify the application of ChemiRs to search by chemicals. We applied ChemiRs to analyze diethylhexyl phthalate (DEHP) by submitting ‘DEHP’ in ‘Search by chemical’ module. After pressing the ‘Refresh’ button, we clicked the Medical Subject Heading (MeSH) ID ‘D004051, Diethylhexyl Phthalate’ and chose ‘None’ as the filter; ‘miRNAs,’ ‘Genes,’ ‘Diseases,’ ‘Pathways,’ and ‘GO terms’ as the output functions; all ten methods as miRNA target prediction methods, and ‘10 minimum predicted methods’ as restrictions, respectively. As shown in Fig. 5, the results can be easily downloaded as CSV files.Fig. 5

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.

ABSTRACT

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 .

No MeSH data available.


Related in: MedlinePlus