Table 4 Genes from the GWAS meta-analysis set involved in the Experimental_brain-specific network that were classified into Rank_2: genes without biological interpretation and their first neighbors
Genes from the GWAS meta-analysis set | First neighbor(s) | Association | ||||||
|---|---|---|---|---|---|---|---|---|
Gene | RNA tissue category/DEGaor TSEA geneb | GWAS meta-analysis paper | Lead SNP | Gene/Data source | Number of neighbors/Rankc | RNA tissue category/DEGa or TSEA geneb | Quality of evidence | Comment |
ETV5 | Expressed in all/DEG | [30] [29] | rs9816226 rs1516725 | AR/OMIM_all_text | 10/3 | Expressed in all/DEG | Very high | ETV5 (ERM) and AR were found interacting in humans [91] |
LRP1B | Group enriched/DEG and TSEA | [30] [29] | rs2890652 rs2121279 | SERPINE1/OMIM_all_text | 1/12 | Tissue enhanced/DEG | Very high | LRP1B and SERPINE1(=PAI-1) were found interacting in humans [96]. |
NDUFS3 | Expressed in all/DEG | [30] | rs3817334 | ADRB2/OMIM_allelic _variants PARK2/GWAS meta-analysis | 7/6 8/5 | Mixed/DEG Tissue enhanced/DEG | Very high Medium | NDUFS3d and ADRB2 were found interacting in humans [103]. Human NDUFS3 interact with PARK2 through one intermediate protein [104]. |
SNRPC | Expressed in all/DEG | [29] | rs205262 | TOMM40/GWAS meta-analysis SNRPN/Syndrome | 2/11 1/12 | Expressed in all/DEG Expressed in all/TSEA | Medium Medium | Interaction in humans has been curated in BioGRID interaction database on the base of [105], but it was not found in the main text of the article or in Suppl. files Putative homologs of human SNRPC and SNRPN were found interacting in yeast [106] |
ERBB4 | Group enriched/TSEA | [29] | rs7599312 | STAT3/OMIM_all_text | 10/3 | Expressed in all/DEG | Medium | Putative homologs (ErbB-2 and Stat3) were found interacting in mice [107] |
PRKD1 | Mixed/DEG | [30] [29] | rs11847697 rs12885454 rs11847697 | MAPK9/OMIM_all_text | 4/9 | Expressed in all/TSEA | Medium | Human PRKD1 (=PKD) and MAPK8 (=JNK), which is MAPK9 homolog, were found interacting in humans [108] |