Table 4.
Enrichment within human-specific genomic regulatory networks (GRNs) of 8405 genes associated with human-specific neuro-regulatory single nucleotide changes (hsSNCs)
| Classification category | Number of genes | Genes associated with hsSNCs |
|---|---|---|
| Networks of genes associated with expression of transposable elements (TE) in human dorsolateral prefrontal cortex | ||
| Human genome | 63,677 | 8405 |
| Networks of genes associated with human DLPFC-expressed TE | 22,863 | 6547 |
| Percent | 35.9 | 77.89 |
| Enrichment** | 1 | 2.17 |
| p value* | 0 | |
| GES of the multi-lineage markers expressing (MLME) cells of human preimplantation embryo | ||
| Human genome | 63,677 | 8405 |
| GES of the MLME cells of human preimplantation embryo | 12,735 | 5218 |
| Percent | 20 | 62.08 |
| Enrichment** | 1 | 3.10 |
| p value* | 0 | |
| Regulatory networks of genes associated with human-specific structural variants*** | ||
| Human genome | 63,677 | 8405 |
| Genes associated with human-specific deletions and insertions | 10,992 | 3056 |
| Percent | 17.26 | 36.36 |
| Enrichment** | 1 | 2.11 |
| p value* | 0 | |
| Gene expression signature of the HERVH/LBP9 network in hESC | ||
| Human genome | 63,677 | 8405 |
| Genes associated with the HERVH/LBP9 pathway in hESC | 11,507 | 4073 |
| Percent | 18.07 | 48.46 |
| Enrichment** | 1 | 2.68 |
| p value* | 0 | |
| Network of genes associated with regulatory TE in naïve and primed hESC | ||
| Human genome | 63,677 | 8405 |
| Genes associated with regulatory TE in naïve and primed hESC | 6148 | 2787 |
| Percent | 9.65 | 33.16 |
| Enrichment** | 1 | 3.44 |
| p value* | 0 | |
| Network of genes differentially expressed in human fetal brain and adult neocortex | ||
| Human genome | 63,677 | 8405 |
| Human fetal brain/adult neocortex signature genes | 4764 | 2448 |
| Percent | 7.48 | 29.13 |
| Enrichment** | 1 | 3.89 |
| p value* | 0 | |
| Human neurogenesis in vivo network^ | ||
| Human genome | 63,677 | 8405 |
| Gene expression signatures of human neurogenesis in vivo | 11,911 | 5467 |
| Percent | 18.71 | 65.04 |
| Enrichment** | 1 | 3.48 |
| p value* | 0 | |
| Human corticogenesis in vitro network | ||
| Human genome | 63,677 | 8405 |
| Gene expression signatures of human corticogenesis in vitro | 12,334 | 5253 |
| Percent | 19.37 | 62.50 |
| Enrichment** | 1 | 3.23 |
| p value* | 0 | |
Human-specific genomic regulatory networks (GRNs) were defined previously (Glinsky, 2020a, see text for details) based on the following primary contributions:
Networks of genes associated with expression of transposable elements (TE) in human dorsolateral prefrontal cortex: Guffanti et al. (2018)
Gene expression signature (GES) of the multi-lineage markers expressing (MLME) cells of human preimplantation embryo: Glinsky et al. (2018)
Regulatory networks of genes associated with human-specific structural variants: Kronenberg et al. (2018)
Gene expression signature of the HERVH/LBP9 network in hESC: Wang et al. (2014)
Network of genes associated with regulatory TE in naïve and primed hESC: Theunissen et al. (2016)
Network of genes differentially expressed in human fetal brain and adult neocortex: Glinsky (2017). doi: 10.1101/022913
Human neurogenesis in vivo network: Nowakowski et al. (2017)
Human corticogenesis in vitro network: van de Leemput et al. (2014)
TE transposable genetic elements, hESC human embryonic stem cell, DLPFC dorsolateral prefrontal cortex, MLME multi lineage markers expression
*p values were estimate using the hypergeometric distribution test
**Expected values were estimated based on the number of genes in the human genome (63,677) and the number of genes in the corresponding category of human-specific regulatory networks
***This category of genes was reported in Kronenberg et al. (2018)
^This category of genes was reported in Nowakowski et al. (2017)