miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature

BackgroundMicroRNAs have been discovered as important regulators of gene expression. To identify the target genes of microRNAs, several databases and prediction algorithms have been developed. Only few experimentally confirmed microRNA targets are available in databases. Many of the microRNA targets stored in databases were derived from large-scale experiments that are considered not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories.ResultsThe microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene and protein occurrences as well as their relationships from texts. Thereby, we increased the number of human, mouse and rat miRNA-gene associations by at least three-fold as compared to e.g. TarBase, a resource for miRNA-gene associations.ConclusionsOur database miRSel offers the currently largest collection of literature derived miRNA-gene associations. Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms. miRSel is freely available online at http://services.bio.ifi.lmu.de/mirsel.

[1]  U. A. Ørom,et al.  Experimental identification of microRNA targets. , 2010, Gene.

[2]  A. Armugam,et al.  MicroRNA Expression in the Blood and Brain of Rats Subjected to Transient Focal Ischemia by Middle Cerebral Artery Occlusion , 2008, Stroke.

[3]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[4]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[5]  Emden R. Gansner,et al.  An open graph visualization system and its applications to software engineering , 2000, Softw. Pract. Exp..

[6]  Olivier Voinnet,et al.  Revisiting the principles of microRNA target recognition and mode of action , 2009, Nature Reviews Molecular Cell Biology.

[7]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[8]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[9]  Sue Povey,et al.  The HGNC Database in 2008: a resource for the human genome , 2007, Nucleic Acids Res..

[10]  Yitzhak Pilpel,et al.  Differentially Regulated Micro-RNAs and Actively Translated Messenger RNA Transcripts by Tumor Suppressor p53 in Colon Cancer , 2006, Clinical Cancer Research.

[11]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[12]  W. Ritchie,et al.  Predicting microRNA targets and functions: traps for the unwary , 2009, Nature Methods.

[13]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[14]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[15]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[16]  C. Croce,et al.  MiR-15a and miR-16-1 cluster functions in human leukemia , 2008, Proceedings of the National Academy of Sciences.

[17]  Sanghyuk Lee,et al.  miRGator: an integrated system for functional annotation of microRNAs , 2007, Nucleic Acids Res..

[18]  Yi-Hsuan Chen,et al.  miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes , 2007, Nucleic Acids Res..

[19]  Ralf Zimmer,et al.  A simple approach for protein name identification: prospects and limits , 2005, BMC Bioinformatics.

[20]  P. Bork,et al.  Literature mining for the biologist: from information retrieval to biological discovery , 2006, Nature Reviews Genetics.

[21]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[22]  Christian Blaschke,et al.  Status of text-mining techniques applied to biomedical text. , 2006, Drug discovery today.

[23]  Ralf Zimmer,et al.  Gene and protein nomenclature in public databases , 2006, BMC Bioinformatics.

[24]  Qizhi Yao,et al.  MicroRNAs: Control and Loss of Control in Human Physiology and Disease , 2009, World Journal of Surgery.

[25]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[26]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[27]  A. Hatzigeorgiou,et al.  A combined computational-experimental approach predicts human microRNA targets. , 2004, Genes & development.

[28]  Martin Reczko,et al.  The database of experimentally supported targets: a functional update of TarBase , 2008, Nucleic Acids Res..

[29]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[30]  Sophia Ananiadou,et al.  Text mining and its potential applications in systems biology. , 2006, Trends in biotechnology.

[31]  Xiaowei Wang.  miRDB: a microRNA target prediction and functional annotation database with a wiki interface. , 2008, RNA.

[32]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[33]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): mouse biology and model systems , 2007, Nucleic Acids Res..

[34]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[35]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[36]  Mark A. Ragan,et al.  Transcriptome-Wide Prediction of miRNA Targets in Human and Mouse Using FASTH , 2009, PloS one.

[37]  A. Hatzigeorgiou,et al.  TarBase: A comprehensive database of experimentally supported animal microRNA targets. , 2005, RNA.

[38]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[39]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[40]  Daniel Hanisch,et al.  ProMiner: rule-based protein and gene entity recognition , 2005, BMC Bioinformatics.

[41]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[42]  Timos K. Sellis,et al.  miRGen 2.0: a database of microRNA genomic information and regulation , 2009, Nucleic Acids Res..

[43]  BMC Bioinformatics , 2005 .

[44]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[45]  Alfred V. Aho,et al.  Efficient string matching , 1975, Commun. ACM.

[46]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..