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

Peggy I. Wang, Sohyun Hwang, Rodney P. Kincaid, Christopher S. Sullivan, Insuk Lee, Edward M. Marcotte

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)R125
JournalGenome biology
Volume13
Issue number12
DOIs
Publication statusPublished - 2012

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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