Table 2.
Gene ontology (GO) terms significantly overrepresented (p < 0.001, 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 | p 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 | ||