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

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

Research output: Contribution to journalShort surveypeer-review

5 Scopus citations


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
Issue number37
StatePublished - Sep 7 2012
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


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