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Table 1 Statistical parameters derived from the study of the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

From: Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

TF Description (SGD database) # targets KS value p-val p-val (adjusted)
STB4 Putative transcription factor; contains a Zn(II)2Cys6 zinc finger domain characteristic of DNA-binding proteins; computational analysis suggests a role in regulation of expression of genes encoding transporters; binds Sin3p in a two-hybrid assay 32 0.166 2e−12 3e−10
AZF1 Zinc-finger transcription factor; involved in diauxic shift; in the presence of glucose, activates transcription of genes involved in growth and carbon metabolism; in nonfermentable carbon sources, activates transcription of genes involved in maintenance of cell wall integrity; relocalizes to the cytosol in response to hypoxia 52 0.153 1e−27 1e−25
MOT3 Transcriptional repressor, activator; role in cellular adjustment to osmotic stress including modulation of mating efficiency; involved in repression of subset of hypoxic genes by Rox1p, repression of several DAN/TIR genes during aerobic growth, ergosterol biosynthetic genes in response to hyperosmotic stress; contributes to recruitment of Tup1p-Cyc8p general repressor to promoters; relocalizes to cytosol under hypoxia; forms [MOT3+] prion under anaerobic conditions 56 0.144 2e−28 5e−26
UPC2 Sterol regulatory element binding protein; induces sterol biosynthetic genes, upon sterol depletion; acts as a sterol sensor, binding ergosterol in sterol rich conditions; relocates from intracellular membranes to perinuclear foci upon sterol depletion; redundant activator of filamentation with ECM22, up-regulating the expression of filamentous growth genes; contains a Zn[2]-Cys[6] binuclear cluster; UPC2 has a paralog, ECM22, that arose from the whole genome duplication 38 0.106 2e−07 4e−05
PHO2 Homeobox transcription factor; regulatory targets include genes involved in phosphate metabolism; binds cooperatively with Pho4p to the PHO5 promoter; phosphorylation of Pho2p facilitates interaction with Pho4p; relocalizes to the cytosol in response to hypoxia 134 0.100 6e−78 1e−75
DAL80 Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with Gzf3p; DAL80 has a paralog, GZF3, that arose from the whole genome duplication 57 0.097 1e−13 2e−11
YAP3 Basic leucine zipper (bZIP) transcription factor 39 0.095 2e−06 0.0004
PLM2 Putative transcription factor, contains Forkhead Associated domain; found associated with chromatin; target of SBF transcription factor; induced in response to DNA damaging agents and deletion of telomerase; PLM2 has a paralog, TOS4, that arose from the whole genome duplication 182 0.093 5e−125 9e−123
RSF2 Zinc-finger protein; involved in transcriptional control of both nuclear and mitochondrial genes, many of which specify products required for glycerol-based growth, respiration, and other functions; RSF2 has a paralog, TDA9, that arose from the whole genome duplication; relocalizes from nucleus to cytoplasm upon DNA replication stress 35 0.092 7e−05 0.012
RPH1 JmjC domain-containing histone demethylase; targets tri- and dimethylated H3K36; associates with actively transcribed regions and promotes elongation; repressor of autophagy-related genes in nutrient-replete conditions; damage-responsive repressor of PHR1; phosphorylated by the Rad53p-dependent DNA damage checkpoint pathway and by a Rim1p-mediated event during starvation; target of stress-induced hormesis; RPH1 has a paralog, GIS1, that arose from the whole genome duplication 91 0.090 7e−30 1e−27
  1. The ten TFs with the highest values of KS statistics are shown here. Results for all other TFs are available as Additional file 4