TY - JOUR
T1 - Genomic regression analysis of coordinated expression
AU - Cai, Ling
AU - Li, Qiwei
AU - Du, Yi
AU - Yun, Jonghyun
AU - Xie, Yang
AU - Deberardinis, Ralph J.
AU - Xiao, Guanghua
N1 - Publisher Copyright:
© 2017 The Author(s).
PY - 2017/12/1
Y1 - 2017/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-017-02181-0
DO - 10.1038/s41467-017-02181-0
M3 - Article
C2 - 29259170
AN - SCOPUS:85038613030
SN - 2041-1723
VL - 8
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 2187
ER -