Expression-based monitoring of transcription factor activity: the TELiS database

Bioinformatics
Steve W ColeJerome A Zack

Abstract

In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity. In two validation studies, TELiS accurately detected in vivo activation of NF-kappaB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoi...Continue Reading

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Citations

Jul 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·Gregory E MillerMichael S Kobor
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Steven W ColeTeresa E Seeman
Nov 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Steven W ColeStephen J Suomi
Jul 31, 2013·Proceedings of the National Academy of Sciences of the United States of America·Barbara L FredricksonSteven W Cole
Jan 18, 2013·Algorithms for Molecular Biology : AMB·Songjian Lu, Xinghua Lu
Sep 15, 2007·Genome Biology·Steve W ColeJohn T Cacioppo
Apr 13, 2011·PloS One·Apostolos ZaravinosDemetrios A Spandidos
Jun 21, 2013·PloS One·Daniel VaimanFrancisco Miralles
May 6, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Sama F SleimanRajiv R Ratan
Aug 10, 2013·American Journal of Public Health·Steven W Cole
Jun 1, 2009·Current Directions in Psychological Science·Steve W Cole
Dec 20, 2005·Expert Review of Molecular Diagnostics·Xiaofeng ZhouDavid T W Wong
Nov 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Steven W ColeJohn T Cacioppo
Jan 13, 2016·Reproduction : the Official Journal of the Society for the Study of Fertility·Catherina A CuevasHoracio B Croxatto
Nov 7, 2012·Neuroscience and Biobehavioral Reviews·Aoife O'DonovanThomas C Neylan
Jul 16, 2010·Psychoneuroendocrinology·Steve W Cole
May 9, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Rubén ArmañanzasAna M Zubiaga
Nov 18, 2011·Biological Psychiatry·Michael H AntoniSteven W Cole
Apr 7, 2009·Brain Research·Dirk A RidderMarkus Schwaninger
Nov 16, 2012·The Journal of General Virology·Carolyn Z GrimesEric L Brown
Jun 13, 2015·Journal of Applied Toxicology : JAT·Sabrina TaitAlberto Mantovani
Dec 5, 2012·Brain, Behavior, and Immunity·Steven W Cole
Jun 14, 2008·Brain, Behavior, and Immunity·Susan K LutgendorfSteve W Cole
Dec 3, 2014·Psychoneuroendocrinology·Kavita VedharaSteven W Cole
Dec 17, 2011·Psychoneuroendocrinology·Andrew W BergenJudy A Andrews
Jan 2, 2014·Brain, Behavior, and Immunity·Mary-Frances O'ConnorSteven W Cole

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