Uncovering transcription factor modules using one- and three-dimensional analyses

Xun Lan, Peggy J. Farnham, Victor X. Jin

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Transcriptional regulation is a critical mediator of many normal cellular processes, as well as disease progression. Transcription factors (TFs) often co-localize at cis-regulatory elements on the DNA, form protein complexes, and collaboratively regulate gene expression. Machine learning and Bayesian approaches have been used to identify TF modules in a one-dimensional context. However, recent studies using high throughput technologies have shown that TF interactions should also be considered in three-dimensional nuclear space. Here, we describe methods for identifying TF modules and discuss how moving from a one-dimensional to a three-dimensional paradigm, along with integrated experimental and computational approaches, can lead to a better understanding of TF association networks.

Original languageEnglish (US)
Pages (from-to)30914-30921
Number of pages8
JournalJournal of Biological Chemistry
Volume287
Issue number37
DOIs
StatePublished - Sep 7 2012
Externally publishedYes

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Transcription Factors
Bayes Theorem
Gene expression
Disease Progression
Learning systems
Throughput
Technology
Gene Expression
DNA
Proteins

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Uncovering transcription factor modules using one- and three-dimensional analyses. / Lan, Xun; Farnham, Peggy J.; Jin, Victor X.

In: Journal of Biological Chemistry, Vol. 287, No. 37, 07.09.2012, p. 30914-30921.

Research output: Contribution to journalArticle

Lan, Xun ; Farnham, Peggy J. ; Jin, Victor X. / Uncovering transcription factor modules using one- and three-dimensional analyses. In: Journal of Biological Chemistry. 2012 ; Vol. 287, No. 37. pp. 30914-30921.
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