RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene networkReportar como inadecuado




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Genome Biology

, 13:R125

First Online: 26 December 2012Received: 27 June 2012Revised: 01 August 2012Accepted: 26 December 2012

Abstract

The growing availability of large-scale functional networks has promoted the development of many successful techniques for predicting functions of genes. Here we extend these network-based principles and techniques to functionally characterize whole sets of genes. We present RIDDLE Reflective Diffusion and Local Extension, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. RIDDLE is particularly adept at characterizing sets with no annotations, a major challenge where most traditional set analyses fail. Notably, RIDDLE found microRNA-450a to be strongly implicated in ocular diseases and development. A web application is available at http:-www.functionalnet.org-RIDDLE.

AbbreviationsAPaverage precision

AUCarea under the ROC curve

Eembryonic day

GBAguilt-by-association

GOGene Ontology

KEGGKyoto Encyclopedia of Genes and Genomes

LElocal extension

miRNAmicroRNA

Ppostnatal day

RASRIDDLE association score

RDreflective diffusion

RIDDLEReflective Diffusion and Local Extension

SVMsupport vector machine.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2012-13-12-r125 contains supplementary material, which is available to authorized users.

Peggy I Wang, Sohyun Hwang contributed equally to this work.

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Autor: Peggy I Wang - Sohyun Hwang - Rodney P Kincaid - Christopher S Sullivan - Insuk Lee - Edward M Marcotte

Fuente: https://link.springer.com/



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