Microarray-Based Identification of Transcription Factor Target Genes

2011 ◽  
pp. 119-141 ◽  
Author(s):  
Maartje Gorte ◽  
Anneke Horstman ◽  
Robert B. Page ◽  
Renze Heidstra ◽  
Arnold Stromberg ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Transcription Factor Target

Analysis of steric effects in DamID profiling of transcription factor target genes

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 75-82 ◽  
Author(s):  
Mirana Ramialison ◽  
Ashley J. Waardenberg ◽  
Nicole Schonrock ◽  
Tram Doan ◽  
Danielle de Jong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Steric Effects ◽  
Transcription Factor Target

scholarly journals Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

2014 ◽  
Vol 31 (6) ◽  
pp. 761-773 ◽  
Author(s):  
Emily Clough ◽  
Erin Jimenez ◽  
Yoo-Ah Kim ◽  
Cale Whitworth ◽  
Megan C. Neville ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Tissue Specific ◽  
Transcription Factor Target

scholarly journals Seed-based systematic discovery of specific transcription factor target genes

FEBS Journal ◽  
2008 ◽  
Vol 275 (12) ◽  
pp. 3178-3192 ◽  
Author(s):  
Ralf Mrowka ◽  
Nils Blüthgen ◽  
Michael Fähling
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Specific Transcription Factor ◽  
Transcription Factor Target

scholarly journals Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2823
Author(s):  
Ian M. Overton ◽  
Andrew H. Sims ◽  
Jeremy A. Owen ◽  
Bret S. E. Heale ◽  
Matthew J. Ford ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Networks ◽  
Epithelial To Mesenchymal Transition ◽  
Target Genes ◽  
Cell Model ◽  
Tumour Progression ◽  
Mesenchymal Transition ◽  
Transcription Factor Target ◽  
Network Modules ◽  
Conserved Gene

Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted “neutral” (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington’s epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.

scholarly journals Targetfinder.org: a resource for systematic discovery of transcription factor target genes

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W233-W238 ◽  
Author(s):  
S. M. Kielbasa ◽  
N. Bluthgen ◽  
M. Fahling ◽  
R. Mrowka
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Transcription Factor Target

scholarly journals Seed based systematic discovery of specific transcription factor target genes

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
Ralf Mrowka ◽  
Nils Blüthgen ◽  
Szymon Kielbasa ◽  
Pontus Börje Persson ◽  
Michael Fähling
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Specific Transcription Factor ◽  
Transcription Factor Target
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