Using networks to measure similarity between genes: association index selection
Program in Systems Biology; Program in Molecular Medicine
Computational Biology | Genetics and Genomics | Systems Biology
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.
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Citation: Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nat Methods. 2013 Nov 26;10(12):1169-76. doi: 10.1038/nmeth.2728. Link to article on publisher's site
Fuxman Bass, Juan I.; Diallo, Alos; Nelson, Justin; Soto, Juan M.; Myers, Chad L.; and Walhout, Albertha J. M., "Using networks to measure similarity between genes: association index selection" (2013). Program in Systems Biology Publications and Presentations. 34.