An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules

Huaxia Qin, Michael W Y Chan, Sandya Liyanarachchi, Curtis Balch, Dustin Potter, Irene J. Souriraj, Alfred S L Cheng, Francisco J. Agosto-Perez, Elena V. Nikonova, Pearlly S. Yan, Huey Jen Lin, Kenneth Nephew, Joel H. Saltz, Louise C. Showe, Tim H M Huang, Ramana V. Davuluri

Research output: Contribution to journalArticle

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Abstract

Background: The TGF-β/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-β/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context. Results: To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-β/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-β activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1). Conclusion: Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules.

Original languageEnglish
Article number73
JournalBMC Systems Biology
Volume3
DOIs
StatePublished - Jul 17 2009

Fingerprint

Transcription factors
Gene Expression Profiling
Profiling
Gene expression
Gene Expression
Chip
T Cell Transcription Factor 1
Transcription Factors
Binding Sites
Binding sites
Module
Data Mining
Chromatin Immunoprecipitation
Microarray Analysis
Transcription Factor
Genes
Epithelium
Microarrays
Crosstalk
Messenger RNA

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Applied Mathematics
  • Modeling and Simulation
  • Computer Science Applications

Cite this

Qin, H., Chan, M. W. Y., Liyanarachchi, S., Balch, C., Potter, D., Souriraj, I. J., ... Davuluri, R. V. (2009). An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. BMC Systems Biology, 3, [73]. https://doi.org/10.1186/1752-0509-3-73

An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. / Qin, Huaxia; Chan, Michael W Y; Liyanarachchi, Sandya; Balch, Curtis; Potter, Dustin; Souriraj, Irene J.; Cheng, Alfred S L; Agosto-Perez, Francisco J.; Nikonova, Elena V.; Yan, Pearlly S.; Lin, Huey Jen; Nephew, Kenneth; Saltz, Joel H.; Showe, Louise C.; Huang, Tim H M; Davuluri, Ramana V.

In: BMC Systems Biology, Vol. 3, 73, 17.07.2009.

Research output: Contribution to journalArticle

Qin, H, Chan, MWY, Liyanarachchi, S, Balch, C, Potter, D, Souriraj, IJ, Cheng, ASL, Agosto-Perez, FJ, Nikonova, EV, Yan, PS, Lin, HJ, Nephew, K, Saltz, JH, Showe, LC, Huang, THM & Davuluri, RV 2009, 'An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules', BMC Systems Biology, vol. 3, 73. https://doi.org/10.1186/1752-0509-3-73
Qin, Huaxia ; Chan, Michael W Y ; Liyanarachchi, Sandya ; Balch, Curtis ; Potter, Dustin ; Souriraj, Irene J. ; Cheng, Alfred S L ; Agosto-Perez, Francisco J. ; Nikonova, Elena V. ; Yan, Pearlly S. ; Lin, Huey Jen ; Nephew, Kenneth ; Saltz, Joel H. ; Showe, Louise C. ; Huang, Tim H M ; Davuluri, Ramana V. / An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. In: BMC Systems Biology. 2009 ; Vol. 3.
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abstract = "Background: The TGF-β/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-β/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context. Results: To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-β/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-β activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1). Conclusion: Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules.",
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AU - Balch, Curtis

AU - Potter, Dustin

AU - Souriraj, Irene J.

AU - Cheng, Alfred S L

AU - Agosto-Perez, Francisco J.

AU - Nikonova, Elena V.

AU - Yan, Pearlly S.

AU - Lin, Huey Jen

AU - Nephew, Kenneth

AU - Saltz, Joel H.

AU - Showe, Louise C.

AU - Huang, Tim H M

AU - Davuluri, Ramana V.

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