A Supervised Network Analysis on Gene Expression Profiles of Breast Tumors Predicts a 41-Gene Prognostic Signature of the Transcription FactorMYBacross Molecular Subtypes

Abstract

Background. MYBis predicted to be a favorable prognostic predictor in a breast cancer population. We proposed to find the inferred mechanism(s) relevant to the prognostic features ofMYBvia a supervised network analysis.Methods. Both coefficient of intrinsic dependence (CID) and Galton Pierson’s correlation coefficient (GPCC) were combined and designated as CIDUGPCC. It is for the univariate network analysis. Multivariate CID is for the multivariate network analysis. Other analyses using bioinformatic tools and statistical methods are included.Results. ARNT2is predicted to be the essential gene partner ofMYB. We classified four prognostic relevant gene subpools in three breast cancer cohorts as feature types I–IV. Only the probes in feature type II are the potential prognostic feature ofMYB. Moreover, we further validated 41 prognosis relevant probes to be the favorable prognostic signature. Surprisingly, two additional family members ofMYBare elevated to promote poor prognosis when both levels ofMYBandARNT2decline. BothMYBL1andMYBL2may partially decrease the tumor suppressive activities that are predicted to be up-regulated byMYBandARNT2.Conclusions. The major prognostic feature ofMYBis predicted to be determined by theMYBsubnetwork (41 probes) that is relevant across subtypes.