title: Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis.
abstract: Transcription factor activity is largely regulated through post-translational modification. Here, we report the first integrative model of transcription that includes both interactions between transcription factors and promoters, and between transcription factors and modifying enzymes. Simulations indicate that our method is robust against noise. We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription.
authors.affiliation: Genomics and Computational Biology Program, 700 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA. loganje@mail.med.upenn.edu
authors.forename: Logan J
authors.initials: LJ
authors.lastname: Everett
authors.forename: Shane T
authors.initials: ST
authors.lastname: Jensen
authors.forename: Sridhar
authors.initials: S
authors.lastname: Hannenhalli
mesh_terms: D001402:B-Lymphocytes / Q000201:enzymology / Q000378:metabolism; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011494:Protein Kinases / Q000378:metabolism; D050794:STAT1 Transcription Factor / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; C081935:MSN2 protein, S cerevisiae; C081937:MSN4 protein, S cerevisiae; D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D011494:Protein Kinases