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Functional & Integrative Genomics

, Volume 19, Issue 1, pp 191–204 | Cite as

Integrated analysis of transcription factors and targets co-expression profiles reveals reduced correlation between transcription factors and target genes in cancer

  • Jinsheng Liang
  • Ying Cui
  • Yuhuan Meng
  • Xingsong Li
  • Xueping Wang
  • Wanli Liu
  • Lizhen Huang
  • Hongli DuEmail author
Original Article
  • 106 Downloads

Abstract

Transcription factors are recognized as the key regulators of gene expression. However, the changes in the correlation of transcription factors and their target genes between normal and tumor tissues are usually ignored. In this research, we used mRNA expression profile data from The Cancer Genome Atlas which included 5726 samples across 11 major human cancers to perform co-expression analysis by the Pearson correlation coefficients. Then, integrating 81,357 pairs of transcription factors and target genes from transcription factors databases to find out the changes in the co-expression correlation of these gene pairs from normal to tumor tissues. Based on the changes in the number of co-expressed TF-TG pairs and changes in the level of co-expression, we found the generally reduced correlation between transcription factors and their target genes in cancer. Additionally, we screened out universal and specific transcription factors-target genes pairs which may significant influence particular cancer. Then, we obtained 423 cancer cell line expression profiles from Broad Institute Cancer Cell Line Encyclopedia to verify our results. Some of these pairs like XRCC5-XRCC6 have been reported to involve in multiple cancers, while pairs like IRF1-PSMB9 without any previous articles related to tumor but involve in the biological processes of cancer, which are of great potential to be therapeutic targets. Our research may provide insights to better understand the tumor development mechanisms and find potential therapeutic targets.

Keywords

Co-expression Integrative analysis Transcription factor Tumorigenesis Therapeutic target 

Notes

Funding

This work was partially supported by the National key research and development program (SQ2018YFC090062), Science and Technology Planning Project of Guangzhou (201704020176, 201508020040, 201510010044), and the Fundamental Research Funds for the Central Universities (2015ZZ125).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Declaration

We declare that the experiments comply with the current laws of the country in which they were performed.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
  2. 2.Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat-sen University Cancer CenterGuangzhouChina

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