Table 3.

Network level discovery and functional investigation

Network type	Construction method	Discovery	Ref.
lncRNA-miRNA co-expression network	Spearman's correlation calculation for miRNA targeted lncRNA pairs.	The dysregulated network for intra-hepatic cholangiocarcinoma (ICC) was associated with cholesterol homeostasis, insoluble fraction and lipid binding activity.etc.	62
MicroRNA-gene network	MicroRNA and mRNA associated expression and microRNA target prediction	The hsa-miR-96, hsa-miR-1 and hsa-miR-25 are identified as potential therapeutic targets for ICC treatment	63
Gene co-expression network	The regulatory network was constructed by mapping the differentially co-expressed genes to known regulation data.	Several important transcription factors such as, FOXC1, ZIC2, NKX2-2 and GCGR were identified for the future target design.	64
Epithelial-mesenchymal transition (EMT) network in CCA	An extensive overview and summarization of the EMT regulatory network in CCA.	EMT regulatory network from the membrane receptors to the EMT-inducing transcription factors such as, SNAIL, TWIST and ZEB. The plasticity of CCA caused by the redundancies and bypasses of regulating EMT is discussed for the therapeutic challenges.	65