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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

System overview of ChemiRs core framework. All results generated by ChemiRs are deposited in PostgreSQL relational databases and displayed in the visual browser and web page
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Fig2: System overview of ChemiRs core framework. All results generated by ChemiRs are deposited in PostgreSQL relational databases and displayed in the visual browser and web page

Mentions: Schema of the client-server architecture of ChemiRs is shown in Fig. 2. ChemiRs incorporated miRNA target prediction methods and curated databases, including DIANA-microT, miRanda, miRDB, RNAhybrid, PicTar, PITA, RNA22, TargetScan, miRWalk, miRecords, miR2Disease and miRBase as shown in Table 1. Data from the latest versions of all dependent databases are collected and integrated into a relational database in the ChemiRs server. A set of experimentally validated target genes integrated from the miRecords and mirTarBase servers is also integrated in the ChemiRs server. In addition, biological information from CTD, KEGG, REACTOME and Gene Ontology databases were manually curated into ChemiRs. The information is stored in a remote PostgreSQL server which is accessed through a Java Model-View-Controller (MVC) web service design. MyBatis library is used to connect to databases, and data can be retrieved by clients in both text and PDF formats.Fig. 2


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)

System overview of ChemiRs core framework. All results generated by ChemiRs are deposited in PostgreSQL relational databases and displayed in the visual browser and web page
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: System overview of ChemiRs core framework. All results generated by ChemiRs are deposited in PostgreSQL relational databases and displayed in the visual browser and web page
Mentions: Schema of the client-server architecture of ChemiRs is shown in Fig. 2. ChemiRs incorporated miRNA target prediction methods and curated databases, including DIANA-microT, miRanda, miRDB, RNAhybrid, PicTar, PITA, RNA22, TargetScan, miRWalk, miRecords, miR2Disease and miRBase as shown in Table 1. Data from the latest versions of all dependent databases are collected and integrated into a relational database in the ChemiRs server. A set of experimentally validated target genes integrated from the miRecords and mirTarBase servers is also integrated in the ChemiRs server. In addition, biological information from CTD, KEGG, REACTOME and Gene Ontology databases were manually curated into ChemiRs. The information is stored in a remote PostgreSQL server which is accessed through a Java Model-View-Controller (MVC) web service design. MyBatis library is used to connect to databases, and data can be retrieved by clients in both text and PDF formats.Fig. 2

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