A spectral framework to map QTLs affecting joint differential networks of gene co-expression
Fig 4
Joint differential network analysis at snQTL X419 on Chr 18.
(A) Leverage scores for 10000 genes. Primary genes with top 10 leverage are highlighted with transcription IDs. Mitochondrial genome (MT) and scaffold region are coded as Chr 0 and Chr -1, respectively. (B-E) Networks for primary (red annotated nodes) and secondary (orange nodes) genes with top 100 leverages. The edge width indicates the connection strength between two genes; the diameter of node indicates the leverage of the gene; the color indicates enhancement (red) or reduction (blue) of the connection compared with average level. (B) Joint differential network at X419 with top 10% strongly connected edges. A wider edge implies a stronger genetic variation in the co-expression of the gene pair. Most genetic co-expression variations occur between the primary and secondary genes. (C-E) Co-expression networks corresponding to the genotypes GG, RG, and RR at X419, respectively. The linear changes in the colors of edges imply the nearly additive genetic effect to the co-expression networks. novel 1: ENSGACT00000018413; novel 2: ENSGACT00000026589; novel 3: ENSGACT00000017116.