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Nat Methods. 2013 Dec;10(12):1169-76. doi: 10.1038/nmeth.2728.

Using networks to measure similarity between genes: association index selection.

Author information

1
1] Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA. [2] Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

Erratum in

  • Nat Methods. 2014 Mar;11(3):349.

Abstract

Biological networks can be used to functionally annotate genes on the basis of interaction-profile similarities. Metrics known as association indices can be used to quantify interaction-profile similarity. We provide an overview of commonly used association indices, including the Jaccard index and the Pearson correlation coefficient, and compare their performance in different types of analyses of biological networks. We introduce the Guide for Association Index for Networks (GAIN), a web tool for calculating and comparing interaction-profile similarities and defining modules of genes with similar profiles.

PMID:
24296474
PMCID:
PMC3959882
DOI:
10.1038/nmeth.2728
[Indexed for MEDLINE]
Free PMC Article
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