TY - JOUR
T1 - Uncovering transcription factor modules using one- and three-dimensional analyses
AU - Lan, Xun
AU - Farnham, Peggy J.
AU - Jin, Victor X.
N1 - Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.
PY - 2012/9/7
Y1 - 2012/9/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84866139176&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84866139176&partnerID=8YFLogxK
U2 - 10.1074/jbc.R111.309229
DO - 10.1074/jbc.R111.309229
M3 - Short survey
C2 - 22952238
AN - SCOPUS:84866139176
VL - 287
SP - 30914
EP - 30921
JO - Journal of Biological Chemistry
JF - Journal of Biological Chemistry
SN - 0021-9258
IS - 37
ER -