Last updated: 2020-03-08
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For a given trait, prioritization results of network genes are summarized as the following two tables, the first one for network transcription factors (TFs) and the second one for network target genes (TGs).
\(P_1\) columns: posterior probability that at least one SNP within 100 kb of the transcribed region of a given network gene (specified by “Gene”, “Chr.”, “Start” and “End” columns) has non-zero effect on the trait of interest;
“\(P_1^{\sf base}\)”, obtained from fitting RSS-NET baseline model \(M_0\);
“\(P_1^{\sf near}\)”, obtained from fitting RSS-NET enrichment model \(M_1\) to the “near-gene” control network;
“\(P_1^{\sf net}\)”: obtained from fitting RSS-NET enrichment model \(M_1\) to a given gene regulatory network;
“H-distance”: the physical distance, in base pair, between a given network gene and its nearest GWAS hit based on the same GWAS;
“Nearest hit”: the nearest GWAS hit to a given network gene, reported in publication of the same GWAS. The “none” values in this column indicate that there is no published GWAS hit on the same chromosome as the network gene.
Differences between \(P_1^{\sf net}\) and reference \(P_1\) estimates (\(P_1^{\sf base}\) or \(P_1^{\sf near}\)) reflect the influence of regulatory network enrichment on genetic associations, which can help identify putatively new trait-associated genes.