Last updated: 2019-11-07
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Knit directory: rss-peca/
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Prioritization results of network genes are summarized as two tables, one for network transcription factors (TFs) and the other for network target genes (TGs).
P1: 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;
H-distance: the physical distance, in base pair, between a given network gene and its nearest GWAS hit;
Nearest hit: the nearest GWAS hit to a given network gene, reported in the corresponding GWAS publication. The “none” values in this column indicate that there is no published GWAS hit on the same chromosome as the network gene.
Note that Baseline P1 and Enrichment P1 are obtained from fitting RSS-NET baseline and enrichment models respectively. Differences between Baseline P1 and Enrichment P1 reflect the influence of network enrichment on genetic associations, which can help identify putatively new trait-associated genes.
TODO: explain Near-gene P1.