Table 4.

Integrative analyses for the heterogeneous cholangiocarcinoma

Integrative data	Description	Discovery	Ref.
Genetic alterations, gene expression and epigenetics	The samples are clustered to 4 subtypes based on their molecular landscapes which are associated with etiology.	The CCAs could be grouped to fluke-negative or positive clusters and new CCA driver genes/mutations and structural variants were discovered.	2
Copy number, DNA methylation, somatic mutations and RNA expression	Multiple omics data from TCGA are analyzed with cluster ensembles method (CLUE R package).	IDH-mutant enriched subtype has distinct molecular profiles	70
Transcriptional and copy number variation (CNV) data	Reconstruction of CCA associated transcriptional regulatory network, then integrate the CNV to the network and selected the CVN related ICC-TRN.	ICC patients could be clustered to two groups based on the gene expression of nodes in CNV-ICC-TRN.	71
Genome and transcription data	Comparison of Genomic and transcriptional alterations from different populations	CCA with or without liver fluke infection are compared and their similarity and difference are identified	72