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Genomic regression analysis of coordinated expression

Author

Listed:
  • Ling Cai

    (Children’s Medical Center Research Institute at UT Southwestern Medical Center
    Quantitative Biomedical Research Center at UT Southwestern Medical Center)

  • Qiwei Li

    (Quantitative Biomedical Research Center at UT Southwestern Medical Center)

  • Yi Du

    (Department of Bioinformatics at UT Southwestern Medical Center)

  • Jonghyun Yun

    (Department of Mathematics at University of Texas at Arlington)

  • Yang Xie

    (Quantitative Biomedical Research Center at UT Southwestern Medical Center)

  • Ralph J. DeBerardinis

    (Children’s Medical Center Research Institute at UT Southwestern Medical Center)

  • Guanghua Xiao

    (Quantitative Biomedical Research Center at UT Southwestern Medical Center)

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.

Suggested Citation

  • Ling Cai & Qiwei Li & Yi Du & Jonghyun Yun & Yang Xie & Ralph J. DeBerardinis & Guanghua Xiao, 2017. "Genomic regression analysis of coordinated expression," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-02181-0
    DOI: 10.1038/s41467-017-02181-0
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