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Open Access Methodology article

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

Jeff Nie1, Ron Stewart1, Hang Zhang6, James A Thomson1239, Fang Ruan7, Xiaoqi Cui5 and Hairong Wei48*

  • * Corresponding author: Hairong Wei hairong@mtu.edu

  • † Equal contributors

Author Affiliations

1 Morgridge Institute for Research, 330 N. Orchard St., Madison, WI 53715, USA

2 Department of Biostatistics and Medical Informatics, University of Wisconsin, 600 Highland Ave., Madison, WI 53792, USA

3 Department of Cell & Regenerative Biology, University of Wisconsin, 1300 University Ave., Madison, WI 53705, USA

4 School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

5 Department of Mathematics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

6 Department of Computer Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

7 Program of Computing Science and Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

8 Biotechnology Research Center, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

9 Department of Molecular, Cellular, & Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA

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BMC Systems Biology 2011, 5:53  doi:10.1186/1752-0509-5-53

Published: 15 April 2011

Abstract

Background

Identifying the key transcription factors (TFs) controlling a biological process is the first step toward a better understanding of underpinning regulatory mechanisms. However, due to the involvement of a large number of genes and complex interactions in gene regulatory networks, identifying TFs involved in a biological process remains particularly difficult. The challenges include: (1) Most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation, making it difficult to recognize TFs for a biological process; (2) Transcription usually involves several hundred genes that generate a combination of intrinsic noise from upstream signaling networks and lead to fluctuations in transcription; (3) A TF can function in different cell types or developmental stages. Currently, the methods available for identifying TFs involved in biological processes are still very scarce, and the development of novel, more powerful methods is desperately needed.

Results

We developed a computational pipeline called TF-Cluster for identifying functionally coordinated TFs in two steps: (1) Construction of a shared coexpression connectivity matrix (SCCM), in which each entry represents the number of shared coexpressed genes between two TFs. This sparse and symmetric matrix embodies a new concept of coexpression networks in which genes are associated in the context of other shared coexpressed genes; (2) Decomposition of the SCCM using a novel heuristic algorithm termed "Triple-Link", which searches the highest connectivity in the SCCM, and then uses two connected TF as a primer for growing a TF cluster with a number of linking criteria. We applied TF-Cluster to microarray data from human stem cells and Arabidopsis roots, and then demonstrated that many of the resulting TF clusters contain functionally coordinated TFs that, based on existing literature, accurately represent a biological process of interest.

Conclusions

TF-Cluster can be used to identify a set of TFs controlling a biological process of interest from gene expression data. Its high accuracy in recognizing true positive TFs involved in a biological process makes it extremely valuable in building core GRNs controlling a biological process. The pipeline implemented in Perl can be installed in various platforms.