iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
Fig 2
iHerd recovers the hierarchy change within the transcript factor (TF) GRNs.
(a) The UMAP of embeddings for TFs in GM12878. (b) The boxplot of three clusters in GM12878 for the ratio of in degree and out degree. (c) The UMAP of embeddings for TFs in K562. (d) The boxplot of three clusters in K562 for the ratio of in degree and out degree. (e) The UMAP of embeddings for TF2 in GM12878 and K562 without the embedding alignment. (f) The UMAP of embeddings for TF2 in GM12878 and K562 after the embedding alignment. (g) The line plot of the sorted normalized L2 distance. The purple dot indicates there is a switching event for this TF. The boxplot of normalized l2 distance between non-switching TFs and switching TFs also demonstrates that the TF with a higher l2 distance has more chance to switch its cluster from GM12878 to K562. (h-j) The UMAPs of three TF examples switch their cluster from GM12878 to K562.