Document Type

Article

Publication Date

1-17-2015

Publication Title

BioData Mining

Department

Geisel School of Medicine

Abstract

We develop a new concept that reflects how genes are connected based on microarray data using the coefficient of determination (the squared Pearson correlation coefficient). Our gene rank combines a priori knowledge about gene connectivity, say, from the Gene Ontology (GO) database, and the microarray expression data at hand, called the microarray enriched gene rank, or simply gene rank (GR). GR, similarly to Google PageRank, is defined in a recursive fashion and is computed as the left maximum eigenvector of a stochastic matrix derived from microarray expression data. An efficient algorithm is devised that allows computation of GR for 50 thousand genes with 500 samples within minutes on a personal computer using the public domain statistical package R.

DOI

10.1186/s13040-014-0033-1

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