Fig. 5
From: PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies
The \(-\log p\) plots of overlapping and recalled genes after applying PheSeq and sequence analysis in AD, BC, and LC. a Layout of the \(-\log p\) plot. The x-axis and y-axis denote the \(-\log\) p value from the sequence analysis and the PheSeq model respectively. The red line refers to a strict threshold line such as Benjamini FDR in our case, and the green line refers to a less strict threshold line such as \(-\log 0.005\) in our case. Genes are labeled when overlapped in PheSeq and sequence analysis or recalled by PheSeq. b The \(-\log p\) plot of significance for both PheSeq and sequence analysis in AD. Five genes are marked in red, i.e., MAPT, PSEN1, C9orf72, SOD1, and PSEN2. All of them are PheSeq recalled genes, which obtain high significance in PheSeq but obtain less or limited significance in GWAS. c The \(-\log p\) plot in BC. Five PheSeq recalled genes are chosen and marked in red, i.e., NEU1, ZAP70, EIF2S2, ZNRF3, and CLIC11. These genes obtain comparatively higher significance in PheSeq than that in sequence analysis. d The \(-\log p\) plot in LC. The five marked genes are UGT2B15, VPS33B, ATAD5, GNAT2, and SPPL3. All five genes show strong significance in PheSeq but limited significance in sequence analysis