ArticleBMC systems biology2009
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules.
Article in BMC systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Ubiquitin Ligases at the Heart of Skeletal Muscle Atrophy Control.Molecules (Basel, Switzerland) · 2021Review
- PAQR5 Expression Is Suppressed by TGFβ1 and Associated With a Poor Survival Outcome in Renal Clear Cell Carcinoma.Frontiers in oncology · 2021Article
- Identification of Geographic Specific SARS-Cov-2 Mutations by Random Forest Classification and Variable Selection Methods.Statistics and applications · 2020Article
- Autocrine activin A signalling in ovarian cancer cells regulates secretion of interleukin 6, autophagy, and cachexia.Journal of cachexia, sarcopenia and muscle · 2020Article
- The double-edged sword role of fibroblasts in the interaction with cancer cells; an agent-based modeling approach.PloS one · 2020Article
- Network-based integrated analysis of omics data reveal novel players of TGF-β1-induced EMT in human peritoneal mesothelial cells.Scientific reports · 2019Article
- Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.Frontiers in molecular neuroscience · 2019Article
- Lysine‑specific demethylase 2 contributes to the proliferation of small cell lung cancer by regulating the expression of TFPI‑2.Molecular medicine reports · 2018Article
- Smad4 deficiency impairs chondrocyte hypertrophy via the Runx2 transcription factor in mouse skeletal development.The Journal of biological chemistry · 2018Article
- Rewiring of the apoptotic TGF-β-SMAD/NFκB pathway through an oncogenic function of p27 in human papillary thyroid cancer.Oncogene · 2017Article
- Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer.PloS one · 2017Article
- Transcriptional Control by the SMADs.Cold Spring Harbor perspectives in biology · 2016Review
- Stem Cells in the Intestine: Possible Roles in Pathogenesis of Irritable Bowel Syndrome.Journal of neurogastroenterology and motility · 2016Review
- The proto-oncogenic protein TAL1 controls TGF-β1 signaling through interaction with SMAD3.Biochimie open · 2016Article
- TGF-β and the TGF-β Family: Context-Dependent Roles in Cell and Tissue Physiology.Cold Spring Harbor perspectives in biology · 2016Review
- Human epithelial-type ovarian tumour marker beta-2-microglobulin is regulated by the TGF-β signaling pathway.Journal of translational medicine · 2016Article
- Inhibition of breast cancer cell motility with a non-cyclooxygenase inhibitory derivative of sulindac by suppressing TGFβ/miR-21 signaling.Oncotarget · 2016Article
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Authors and funding
16 authors.
Funding
Abstract
backgroundThe TGF-beta/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-beta/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.
resultsTo 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-beta/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-beta 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).
conclusionTogether, 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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