MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression Export

@article{citeulike:4491146, abstract = {MicroRNAs (miRNAs) are small (19-24 nt), nonprotein-coding nucleic acids that regulate specific target' gene products via hybridization to mRNA transcripts, resulting in translational blockade or transcript degradation. Although miRNAs have been implicated in numerous developmental and adult diseases, their specific impact on biological pathways and cellular phenotypes, in addition to miRNA gene promoter regulation, remain largely unknown. To improve and facilitate research of miRNA functions and regulation, we have developed MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server. By incorporating three commonly used and accurate miRNA prediction algorithms, TargetScan, PITA and PicTar, MMIA integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters. To assign biological relevance to the integrated miRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including classification into various disease-associated genes as well as conventional canonical pathways and Gene Ontology. In summary, this novel web server (cancer.informatics.indiana.edu/mmia) will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators. 10.1093/nar/gkp294}, author = {Nam, Seungyoon and Li, Meng and Choi, Kwangmin and Balch, Curtis and Kim, Sun and Nephew, Kenneth P.}, citeulike-article-id = {4491146}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp294}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/gkp294v1/.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/gkp294v1/.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_2/W356?etoc}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19420067}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19420067}, doi = {10.1093/nar/gkp294}, issn = {1362-4962}, journal = {Nucl. Acids Res.}, keywords = {analysis, application, biological, examining, expression, functions, integrated, microrna, mrna, server, site, tool, web, workflow}, month = {May}, number = {Web Server issue}, pages = {gkp294--362}, posted-at = {2009-06-30 10:39:33}, priority = {2}, title = {MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression}, url = {http://dx.doi.org/10.1093/nar/gkp294}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:4491146 L3 - citeulike-article-id:4491146 N2 - MicroRNAs (miRNAs) are small (19-24 nt), nonprotein-coding nucleic acids that regulate specific target' gene products via hybridization to mRNA transcripts, resulting in translational blockade or transcript degradation. Although miRNAs have been implicated in numerous developmental and adult diseases, their specific impact on biological pathways and cellular phenotypes, in addition to miRNA gene promoter regulation, remain largely unknown. To improve and facilitate research of miRNA functions and regulation, we have developed MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server. By incorporating three commonly used and accurate miRNA prediction algorithms, TargetScan, PITA and PicTar, MMIA integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters. To assign biological relevance to the integrated miRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including classification into various disease-associated genes as well as conventional canonical pathways and Gene Ontology. In summary, this novel web server (cancer.informatics.indiana.edu/mmia) will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators. 10.1093/nar/gkp294 IS - Web Server issue JF - Nucl. Acids Res. SN - 1362-4962 EP - 362 TI - MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression VL - 37 SP - gkp294 KW - analysis KW - application KW - biological KW - examining KW - expression KW - functions KW - integrated KW - microrna KW - mrna KW - server KW - site KW - tool KW - web KW - workflow AU - Nam, Seungyoon AU - Li, Meng AU - Choi, Kwangmin AU - Balch, Curtis AU - Kim, Sun AU - Nephew, Kenneth PY - 2009/05/06/ UR - http://dx.doi.org/10.1093/nar/gkp294 ER -