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miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling by C. L. Plaisier; J. C. Bare; N. S. Baliga is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling about?

Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from __Caenorhabditis elegans__, __Drosophila melanogaster__, __G. gallus__, __Homo sapiens__, __Mus musculus__ or __Rattus norvegicus__ and identifies the specific miRNAs that are likely to bind to 3′ un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity __P__-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3′-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for __de novo__ discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of pu

Who reads miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling?

Author

C. L. Plaisier; J. C. Bare; N. S. Baliga

Publisher

Oxford University Press; London: Information Retrieval; Oxford: Oxford University Press; Oxford University Press (OUP) (ISSN 0305-1048)

Published

2011

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)