miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators
Open Access
- 14 December 2011
- journal article
- Published by Springer Science and Business Media LLC in BMC Systems Biology
- Vol. 5 (S2), S9
- https://doi.org/10.1186/1752-0509-5-s2-s9
Abstract
Background In recent years, a number of tools have been developed to explore microRNAs (miRNAs) by analyzing their target genes. However, a reverse problem, that is, inferring patterns of protein-coding genes through their miRNA regulators, has not been explored. As various miRNA annotation data become available, exploring gene patterns by analyzing the prior knowledge of their miRNA regulators is becoming more feasible. Results In this study, we developed a tool, miR2Gene, for this purpose. Various sets of miRNAs, according to prior rules such as function, associated disease, tissue specificity, family, and cluster, were integrated with miR2Gene. For given genes, miR2Gene evaluates the enrichment of the predicted miRNAs that regulate them in each miRNA set. This tool can be used for single genes, multiple genes, and KEGG pathways. For the KEGG pathway, genes with enriched miRNA sets are highlighted according to various rules. We confirmed the usefulness of miR2Gene through case studies. Conclusions miR2Gene represents a novel and useful tool that integrates miRNA knowledge for protein-coding gene analysis. miR2Gene is freely available at http://cmbi.hsc.pku.edu.cn/mir2gene.Keywords
This publication has 23 references indexed in Scilit:
- Human MicroRNA Oncogenes and Tumor Suppressors Show Significantly Different Biological Patterns: From Functions to TargetsPLOS ONE, 2010
- MAGIA, a web-based tool for miRNA and Genes Integrated AnalysisNucleic Acids Research, 2010
- Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseasesBioinformatics, 2010
- Evaluation of ARG protein expression in mature B cell lymphomas compared to non-neoplastic reactive lymph nodeCellular Immunology, 2009
- Analysis of protein tyrosine kinases expression in the melanoma metastases of patients treated with Imatinib Mesylate (STI571, GleevecTM)Journal of Cutaneous Pathology, 2006
- [Therapeutic targets in gastrointestinal stromal tumors].2006
- Macrophage colony-stimulating factor receptor c-fms is a novel target of imatinibBlood, 2005
- Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA TargetsCell, 2005
- MicroRNAs: Genomics, Biogenesis, Mechanism, and FunctionCell, 2004
- The microRNA RegistryNucleic Acids Research, 2004