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	15	5.1E − 04	2.77
		Chromatin assembly or disassembly	31	9.6E − 04	1.85
−700/+100	3,926/2,252	Chromatin organization	75	6.7E − 08	1.89
		Chromosome organization	83	7.2E − 06	1.63
		Chromatin modification	51	6.2E − 05	1.78
		Spermatogenesis	53	3.4E − 04	1.64
		Male gamete generation	53	3.4E − 04	1.64
		Nucleosome organization	22	5.1E − 04	2.26
		Gamete generation	63	7.3E − 04	1.52
		DNA packaging	25	9.2E − 04	2.04
−800/+100	3,287/1,858	Chromatin organization	66	1.4E − 08	2.09
		Chromosome organization	72	2.0E − 06	1.78
		Chromatin modification	44	4.0E − 05	1.92
		Spermatogenesis	47	7.6E − 05	1.83
		Male gamete generation	47	7.6E − 05	1.83
		Nucleosome organization	19	6.0E − 04	2.45
		Gamete generation	53	6.6E − 04	1.61
		Chromatin assembly or disassembly	23	7.8E − 04	2.17
−900/+100	2,821/1,587	Chromatin organization	62	7.2E − 10	2.33
		Chromosome organization	68	6.8E − 08	1.99
		Chromatin modification	41	8.2E − 06	2.12
		Male gamete generation	42	5.9E − 05	1.94
		Spermatogenesis	42	5.9E − 05	1.94
		Nucleosome organization	19	7.2E − 05	2.90
		Chromatin assembly or disassembly	22	2.0E − 04	2.46
		DNA packaging	20	5.0E − 04	2.43
		Gamete generation	47	5.0E − 04	1.69