A guide through present computational approaches for the identification of mammalian microRNA targets.

Full Abstract

Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.

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Author information

Author/s: Sethupathy, Praveen (P); Megraw, Molly (M); Hatzigeorgiou, Artemis G (AG);

Affiliation: Center for Bioinformatics, University of Pennsylvania, Philadelphia Pennsylvania 19104, USA.

Grants: 5T32GM008216 (Agency:NIGMS NIH HHS)

Journal and publication information

Publication Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.

Journal: Nature methods (Nat Methods), published in United States. (Language: eng)

Reference: 2006-Nov; vol 3 (issue 11) : pp 881-6

Dates: Created 2006/10/24; Completed 2007/01/09; Revised 2007/11/14;

PMID: 17060911, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

Comments and Corrections

CommentIn: Nat Methods. 2007 Mar;4(3):191; author reply 191. (PMID: 17327844)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

3' Untranslated Regions - genetics
5' Untranslated Regions - genetics
Animals
Computational Biology - methods
Gene Targeting - methods
Humans

Associated Chemicals: 3' Untranslated Regions (0) ; 5' Untranslated Regions (0) ; MicroRNAs (0) ; RNA, Messenger (0)

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