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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

From: A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

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]
  1. a DEG, differentially expressed gene in mouse hypothalamic AGRP- or POMC-expressing neurons according to [49]
  2. b TSEA gene. Revealed by TSEA (see Gene expression analysis section) as brain-specific at the pSI threshold = 0.05
  3. c The rank was defined for each gene in the network Experimental_brain-specific on the base of the number of first neighbors
  4. d In [103] NDUFS3 was noted as a precursor of NADH-ubiquinone oxidoreductase flavoprotein 3 isoform a (see Supplemental data in [103])