Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data
Table 2
Gene ontology (GO) terms significantly overrepresented (, fold enrichment > 1.5) in the SNP-depleted datasets of human transcripts. Each dataset comprises transcripts that have no SNPs within specific 5′-regulatory regions relative to TSS (first column). The list of overrepresented GO terms was generated by the DAVID tool [22, 23]. Designations of GO terms: italicization means association with transcription, boldface denotes chromatin or chromosome organization, and the regular font points to spermatogenesis and gamete generation.
Location
The total number of transcripts/genes
GO term name
Number of genes involved in the term
value
Fold enrichment
−300/+100
10,488/6,024
Regulation of specific transcription from RNA polymerase II promoter
47
8.2E − 05
1.67
Positive regulation of specific transcription from RNA polymerase II promoter
30
7.4E − 04
1.76
−400/+100
7,799/4,572
Chromatin modification
93
1.4E − 05
1.51
Regulation of specific transcription from RNA polymerase II promoter
38
1.7E − 04
1.80
Positive regulation of specific transcription from RNA polymerase II promoter
25
7.2E − 04
1.95
−500/+100
6,096/3,572
Chromatin organization
105
3.7E − 07
1.60
Negative regulation of transcription, DNA-dependent
99
7.8E − 07
1.61
Chromatin modification
77
9.8E − 06
1.62
Regulation of specific transcription from RNA polymerase II promoter
32
1.6E − 04
1.97
Regulation of gene-specific transcription
41
2.3E − 04
1.77
Negative regulation of transcription from RNA polymerase II promoter
70
2.3E − 04
1.52
−600/+100
4,805/2,786
Chromatin organization
89
4.7E − 08
1.78
Chromosome organization
99
8.3E − 06
1.54
Regulation of specific transcription from RNA polymerase II promoter
29
2.0E − 05
2.33
Negative regulation of transcription, DNA-dependent
76
2.2E − 05
1.61
Chromatin modification
62
2.3E − 05
1.71
Negative regulation of transcription from RNA polymerase II promoter
57
2.4E − 04
1.62
Regulation of gene-specific transcription
34
2.4E − 04
1.92
Negative regulation of gene-specific transcription
17
2.8E − 04
2.68
Negative regulation of specific transcription from RNA polymerase II promoter