SK-HEP-1, SNU-449, SNU-398, SNU-475, and SNU-387 are some of the most widely used cell lines for liver hepatocellular cancer research. Often researchers have questions on selecting the most appropriate cell line(s) for particular research uses.

TumorComparer utilizes several data types (e.g., mutation, copy number, and expression) to perform a comparison of The Cancer Genome Atlas (TCGA) tumor data to experimental cell line models from the Cancer COSMIC Cell Line Project (CCLP) for several cancer types. Please refer to Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039 for details on the methodology.

An analysis for liver hepatocellular cancer cell lines with differences between the liver hepatocellular cancer cell lines SK-HEP-1 vs SNU-449; SK-HEP-1 vs SNU-398; SK-HEP-1 vs SNU-475; and etc.

If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

Characteristics of Liver Hepatocellular Cancer Cell Lines

The figure shows the presence of alterations for genes (TP53, AXIN1, CDKN2A, TERT, CTNNB1, etc.) commonly associated with liver hepatocellular cancer in the cell lines: SNU449, JHH2, JHH6, JHH7, SNU475, etc. The gene list is retrieved from DisGeNET, and the alteration information is retrieved from cBioPortal for the Cancer Cell Line Encyclopedia (CCLE) dataset.

NOTE: Only a subset of liver hepatocellular cancer cell lines are shown to ensure a readable figure. Alterations for additional liver hepatocellular cancer cell lines and genes are available on cBioPortal using links on the table below.

Comparing liver hepatocellular cancer cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

Comparing liver hepatocellular cancer cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

List of Liver Hepatocellular Cancer Cell Lines Compared to Pan-Cancer TCGA

The TumorComparer analysis examines the most variably expressed genes, as well as alteration information for cell lines and TCGA patient data using a weighted similarity approach; for details, read: Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

More information for the liver hepatocellular cancer cell lines is available on cBioPortal using links on the table below.

The table shows liver hepatocellular cancer cell lines sorted by similarity to characteristics of TCGA tumors based on expression, mutation, and copy number information. Cell Lines with higher values of โ€˜% Rank by Avg % Ranksโ€™ are considered better matches.
Cell Line % Rank by Avg % Ranks More Line Info % Rank by Mutation % Rank by Copy Number % Rank by Expression
JHH6 1.00 Link 0.84 0.91 0.98
JHH7 1.00 Link 0.88 0.94 1.00
SNU475 0.98 Link 0.64 0.85 0.97
SNU387 0.97 Link 0.86 0.56 0.98
HUH1 0.95 Link 0.89 0.45 1.00
SNU182 0.95 Link 0.90 0.85 0.56
SNU449 0.91 Link 0.63 0.65 0.92
SNU423 0.86 Link 0.89 0.42 0.77
HUH7 0.82 Link 0.88 0.06 1.00
SNU398 0.77 Link 0.97 0.48 0.39
C3A 0.36 Link 0.19 0.11 1.00
JHH1 0.31 Link 0.11 0.35 0.77
SKHEP1 0.18 Link 0.32 0.33 0.39
HLE 0.02 Link 0.07 0.17 0.30

Cell Lines with Common Mutations Found in TCGA Liver Hepatocellular Cancer

Alterations present in cell lines also present in at least two TCGA Pan-Cancer Atlas (LIHC) samples on cBioPortal.

Alterations

TP53 R249S (TCGA Altered: 3.1%; 11 out of 353 samples)

  • JHH4
  • PLCPRF5

TP53 Y220C (TCGA Altered: 0.6%; 2 out of 353 samples)

  • HUH7

CTNNB1 S37C (TCGA Altered: 0.6%; 2 out of 353 samples)

  • SNU398

Customized Comparisons

Each project has unique questions. TumorComparer (tumorcomparer.org) facilities customized comparisons of cell line datasets to tumor samples directly from the browser.

Technical Information

This analysis was generated using TumorComparer: 0.99.25. If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.