Skip to main content

Table 2 Down- and upregulated genes in scc1-73 cells are associated with a specific chromatin structure at promoters and cohesin peaks, respectively

From: Crosstalk between chromatin structure, cohesin activity and transcription

  OPN
promoter
(544)
DPN
promoter
(494)
Closed
promoter
(1646)
Open
promoter
(3586)
FN
promoter
(1953)
SN
promoter
(3066)
RSC-binding
promoter
(239)
Scc2-
binding
promoter
(199)
TATA-containing
(1090)
SAGA-dominated
(577)
TFIID-dominated
(5130)
Mediator-dominated
(315)*
NuA4-
dominated
(500)*
SWR1-
dominated
(462)
Scc1-binding promoter
(2417)
scc1-73 Up-reg. (569)
 Overlap. 57 51 149 373 222 300 15 16 85 50 467 29 92 41 298
 Obs/exp (p val) 1.2
(0.015)
1.2
(0.021)
1.06
(0.026)
1.22
(1.3e−10)
1.34
(3.5e−8)
1.15
(9e−5)
0.74
(0.045)
0.95
(0.1)
0.92
(0.03)
1.02
(0.06)
1.07
(2.1e−4)
1.08
(0.07)
2.25
(1e−14)
1.04
(0.06)
1.45
(4.9e−17)
scc1-73 Down-reg. (445)
 Overlap. 93 27 153 246 212 202 36 15 166 103 307 53 25 48 136
 Obs/exp (p val) 2.56
(8.8e−19)
0.83
(0.017)
1.4
(4.3e−7)
1
(0.03)
1.63
(7.7e−18)
0.99
(0.039)
2.26
(1.5e−6)
1.13
(0.095)
2.29
(4.2e−29)
2.68
(2e−22)
0.9
(2.7e−5)
2.53
(9.8e−11)
0.78
(0.02)
1.56
(5e−4)
0.85
(1.6e3)
  1. The number of genes in each case is indicated in parentheses. The probability of producing the given overlapping if their distributions were random was generated using a hypergeometric test. The rate between the observed and expected frequencies of common genes is also shown. Significantly higher (underlined) and lower (italics) differences (p value < 0.001) are highlighted in bold.
  2. *Only downregulated genes are analyzed. See Additional file 4: Table S4 for list of genes and references