A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions Export

@article{citeulike:3339203, abstract = {10.1261/rna.1188208 MicroRNAs are short (\^{a}ˆ¼22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA\^{a}€“mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs\^{a}€”above what could be observed in randomly generated gene lists\^{a}€”suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at .}, address = {1The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.}, author = {Creighton, Chad J. and Nagaraja, Ankur K. and Hanash, Samir M. and Matzuk, Martin M. and Gunaratne, Preethi H.}, citeulike-article-id = {3339203}, citeulike-linkout-0 = {http://dx.doi.org/10.1261/rna.1188208}, citeulike-linkout-1 = {http://rnajournal.cshlp.org/content/14/11/2290.abstract}, citeulike-linkout-2 = {http://rnajournal.cshlp.org/content/14/11/2290.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18812437}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18812437}, day = {23}, doi = {10.1261/rna.1188208}, issn = {1469-9001}, journal = {RNA}, keywords = {expression, microrna, tool}, month = {November}, number = {11}, pages = {2290--2296}, posted-at = {2008-09-26 08:52:00}, priority = {2}, title = {A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions}, url = {http://dx.doi.org/10.1261/rna.1188208}, volume = {14}, year = {2008} }

TY - JOUR ID - citeulike:3339203 L3 - citeulike-article-id:3339203 N2 - 10.1261/rna.1188208 MicroRNAs are short (∼22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA–mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs—above what could be observed in randomly generated gene lists—suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at . IS - 11 JF - RNA SN - 1469-9001 AD - 1The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA. EP - 2296 TI - A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions VL - 14 SP - 2290 KW - expression KW - microrna KW - tool AU - Creighton, Chad AU - Nagaraja, Ankur AU - Hanash, Samir AU - Matzuk, Martin AU - Gunaratne, Preethi PY - 2008/11/23/ UR - http://dx.doi.org/10.1261/rna.1188208 ER -