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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