Table 2.

Knowledge based analyses of biological data

Knowledge base	Methods	Discovery	Ref.
Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO)	Enrichment analysis of miRNA targets.	Over-expression of miR-150-5p could inhibit proliferation, migration, and invasion capability of CCA cells and indicate it contributes to the CCA development and progression.	53
	Genome-MuSiC was used to mapping the mutations to the KEGG and NCI pathways and the pathways were clustered and statistically analyzed based on the mutation frequencies.	Several important pathways were identified were identified altered in ICC	54
Connectivity map (CMap), it includes the relationship for drugs, genes and diseases.	A candidate drug is supposed to reverse the gene expression signature of CCA	The HSP90 inhibitor, NVP-AUY922, is screened as a putative effective CCA drug.	52
	Interleukin-6 associated genomic signature in Mz-ChA-1 human malignant cholangiocytes was derived and compounds that induced inverse gene changes to the signature were screened.	Nitrendipine, nifedipine and felodipine that are structurally similar compounds were identified cytotoxic to Mz-ChA-1 cells and could be the potential therapeutic use for CCA.	55