International Journal of Genomics / 2015 / Article / Tab 2

Research Article

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.

LocationThe total number
of transcripts/genes
GO term nameNumber of genes involved in the term valueFold enrichment

−300/+10010,488/6,024Regulation of specific transcription from RNA polymerase II promoter478.2E − 051.67
Positive regulation of specific transcription from RNA polymerase II promoter307.4E − 041.76

−400/+1007,799/4,572Chromatin modification931.4E − 051.51
Regulation of specific transcription from RNA polymerase II promoter381.7E − 041.80
Positive regulation of specific transcription from RNA polymerase II promoter257.2E − 041.95

−500/+1006,096/3,572Chromatin organization1053.7E − 071.60
Negative regulation of transcription, DNA-dependent997.8E − 071.61
Chromatin modification779.8E − 061.62
Regulation of specific transcription from RNA polymerase II promoter321.6E − 041.97
Regulation of gene-specific transcription412.3E − 041.77
Negative regulation of transcription from RNA polymerase II promoter702.3E − 041.52

−600/+1004,805/2,786Chromatin organization894.7E − 081.78
Chromosome organization998.3E − 061.54
Regulation of specific transcription from RNA polymerase II promoter292.0E − 052.33
Negative regulation of transcription, DNA-dependent762.2E − 051.61
Chromatin modification622.3E − 051.71
Negative regulation of transcription from RNA polymerase II promoter572.4E − 041.62
Regulation of gene-specific transcription342.4E − 041.92
Negative regulation of gene-specific transcription172.8E − 042.68
Negative regulation of specific transcription from RNA polymerase II promoter155.1E − 042.77
Chromatin assembly or disassembly319.6E − 041.85

−700/+1003,926/2,252Chromatin organization756.7E − 081.89
Chromosome organization837.2E − 061.63
Chromatin modification516.2E − 051.78
Spermatogenesis533.4E − 041.64
Male gamete generation533.4E − 041.64
Nucleosome organization225.1E − 042.26
Gamete generation637.3E − 041.52
DNA packaging259.2E − 042.04

−800/+1003,287/1,858Chromatin organization661.4E − 082.09
Chromosome organization722.0E − 061.78
Chromatin modification444.0E − 051.92
Spermatogenesis477.6E − 051.83
Male gamete generation477.6E − 051.83
Nucleosome organization196.0E − 042.45
Gamete generation536.6E − 041.61
Chromatin assembly or disassembly237.8E − 042.17

−900/+1002,821/1,587Chromatin organization627.2E − 102.33
Chromosome organization686.8E − 081.99
Chromatin modification418.2E − 062.12
Male gamete generation425.9E − 051.94
Spermatogenesis425.9E − 051.94
Nucleosome organization197.2E − 052.90
Chromatin assembly or disassembly222.0E − 042.46
DNA packaging205.0E − 042.43
Gamete generation475.0E − 041.69