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Genomic regression analysis of coordinated expression.

Abstract：

:Co-expression analysis is widely used to predict gene function and to identify functionally related gene sets. However, co-expression analysis using human cancer transcriptomic data is confounded by somatic copy number alterations (SCNA), which produce co-expression signatures based on physical proximity rather than biological function. To better understand gene-gene co-expression based on biological regulation but not SCNA, we describe a method termed "Genomic Regression Analysis of Coordinated Expression" (GRACE) to adjust for the effect of SCNA in co-expression analysis. The results from analyses of TCGA, CCLE, and NCI60 data sets show that GRACE can improve our understanding of how a transcriptional network is re-wired in cancer. A user-friendly web database populated with data sets from The Cancer Genome Atlas (TCGA) is provided to allow customized query.

journal_name

Nat Commun

journal_title

Nature communications

authors

Cai L,Li Q,Du Y,Yun J,Xie Y,DeBerardinis RJ,Xiao G

doi

10.1038/s41467-017-02181-0

subject

Has Abstract

pub_date

2017-12-19 00:00:00

pages

2187

issue

1

issn

2041-1723

pii

10.1038/s41467-017-02181-0

journal_volume

8

pub_type

杂志文章

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