Identification of interacting transcription factors regulating tissue gene expression in human

BMC Genomics
Zihua Hu, Steven M Gallo


Tissue gene expression is generally regulated by multiple transcription factors (TFs). A major first step toward understanding how tissues achieve their specificity is to identify, at the genome scale, interacting TFs regulating gene expression in different tissues. Despite previous discoveries, the mechanisms that control tissue gene expression are not fully understood. We have integrated a function conservation approach, which is based on evolutionary conservation of biological function, and genes with highest expression level in human tissues to predict TF pairs controlling tissue gene expression. To this end, we have identified 2549 TF pairs associated with a certain tissue. To find interacting TFs controlling tissue gene expression in a broad spatial and temporal manner, we looked for TF pairs common to the same type of tissues and identified 379 such TF pairs, based on which TF-TF interaction networks were further built. We also found that tissue-specific TFs may play an important role in recruiting non-tissue-specific TFs to the TF-TF interaction network, offering the potential for coordinating and controlling tissue gene expression across a variety of conditions. The findings from this study indicate that tissue gene ex...Continue Reading


Apr 6, 2016·Frontiers in Genetics·Sebastian ZeidlerMehmet Gültas
Sep 25, 2014·Bioinformatics and Biology Insights·Sony Malhotra, R Sowdhamini
Aug 25, 2018·PLoS Computational Biology·Alena van BömmelMartin Vingron


Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·L Janson, U Pettersson
Apr 14, 1995·The Journal of Biological Chemistry·L H Shapiro
May 26, 1998·Journal of Molecular Biology·W W Wasserman, J W Fickett
Feb 13, 2001·Mechanisms of Development·S H HsuH Li
Mar 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Feb 28, 2003·The Journal of Biological Chemistry·Teddy T C Yang, Chi-Wing Chow
Jun 26, 2003·Nucleic Acids Research·A E KelEdgar Wingender
Dec 4, 2003·Molecular and Cellular Biology·Sophie MagnéIsabelle Dusanter-Fourt
Feb 28, 2004·Science·Duncan T OdomRichard A Young
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Apr 14, 2004·The Journal of Biological Chemistry·Kai SchuhLudwig Neyses
Apr 5, 2005·Toxicologic Pathology·George A Parker, Catherine A Picut
Aug 2, 2005·Molecular and Cellular Biology·Nir E RubinsKlaus H Kaestner
Dec 31, 2005·Nucleic Acids Research·V MatysEdgar Wingender
Apr 12, 2006·Proceedings of the National Academy of Sciences of the United States of America·Andrew D SmithMichael Q Zhang
Jun 2, 2006·Molecular Systems Biology·Duncan T OdomRichard A Young
Aug 16, 2006·Cellular and Molecular Life Sciences : CMLS·J R Friedman, Klaus H Kaestner
Aug 22, 2006·Experimental Cell Research·Peter J BaileyJohan Ericson
Oct 20, 2006·Bioinformatics·M Juanita MartinezKevin S Harrod
Jan 11, 2007·Genome Research·Len A PennacchioIvan Ovcharenko
Jan 17, 2007·Molecular Systems Biology·Andrew D SmithMichael Q Zhang
Jul 14, 2007·Genome Biology·Domènec FarréM Mar Albà
Oct 11, 2007·Journal of Cell Science·Annette GrohmannJürgen Behrens
Dec 7, 2007·Genome Biology·Zihua HuJames F Collins
Feb 27, 2008·BMC Bioinformatics·Xiaoyu Chen, Mathieu Blanchette
May 15, 2008·Journal of Animal Physiology and Animal Nutrition·P NguyenH Dumon
Jun 21, 2008·The New England Journal of Medicine·Olivera J Finn
Aug 5, 2009·Nucleic Acids Research·Dmitri PapatsenkoMichael Levine

Related Concepts

Ovarian Diseases
ZBTB16 gene
EP300 protein, human
Immune System
Benign Neoplasm of Testis
ARID5B gene
EGR1 gene
Transcriptional Regulation
ALX1 gene
POU3F2 gene

Related Feeds

Basal Ganglia

Basal Ganglia are a group of subcortical nuclei in the brain associated with control of voluntary motor movements, procedural and habit learning, emotion, and cognition. Here is the latest research.