A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity.

ABSTRACT:

Motivation

Tumor tissue samples often contain an unknown fraction of stromal cells. This problem is widely known as tumor purity heterogeneity (TPH) was recently recognized as a severe issue in omics studies. Specifically, if TPH is ignored when inferring co-expression networks, edges are likely to be estimated among genes with mean shift between non-tumor- and tumor cells rather than among gene pairs interacting with each other in tumor cells. To address this issue, we propose Tumor Specific Net (TSNet), a new method which constructs tumor-cell specific gene/protein co-expression networks based on gene/protein expression profiles of tumor tissues. TSNet treats the observed expression profile as a mixture of expressions from different cell types and explicitly models tumor purity p

SUBMITTER: Petralia F 

PROVIDER: S-EPMC6022554 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature