MKN45, NCI-N87, MKN28, HGC-27, and MKN1 are some of the most widely used cell lines for stomach 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 stomach cancer cell lines with differences between the stomach cancer cell lines MKN45 vs NCI-N87; MKN45 vs MKN28; MKN45 vs HGC-27; 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 Stomach Cancer Cell Lines

The figure shows the presence of alterations for genes (ATM, CTNNB1, MLH1, AXL, JAK3, etc.) commonly associated with stomach cancer in the cell lines: KATOIII, SNU1, NUGC4, MKN45, TGBC11TKB, 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 stomach cancer cell lines are shown to ensure a readable figure. Alterations for additional stomach cancer cell lines and genes are available on cBioPortal using links on the table below.

Comparing stomach 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 stomach 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 Stomach 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 stomach cancer cell lines is available on cBioPortal using links on the table below.

The table shows stomach 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
MKN7 0.99 Link 0.94 0.88 0.78
HSC39 0.98 NA 0.94 0.55 0.96
NUGC4 0.98 Link 0.97 0.55 0.95
NCIN87 0.97 Link 0.92 0.60 0.88
MKN45 0.95 Link 0.94 0.37 0.96
SKGT2 0.93 NA 0.94 0.34 0.94
MKN28 0.87 NA 0.30 0.90 0.86
OCUM1 0.87 Link 0.39 0.71 0.98
AGS 0.85 Link 0.29 0.80 0.94
ECC10 0.85 Link 0.33 0.95 0.74
ECC12 0.85 Link 0.92 0.37 0.77
MKN1 0.80 Link 0.55 0.84 0.56
2313287 0.77 Link 0.30 0.65 0.96
HS746T 0.73 Link 0.97 0.60 0.26
SCH 0.69 NA 0.78 0.47 0.50
KATOIII 0.67 Link 0.10 0.65 0.98
NUGC3 0.67 Link 0.45 0.40 0.88
IM9 0.62 NA 0.10 0.95 0.62
RERFGC1B 0.60 Link 0.81 0.34 0.50
HSC3 0.58 NA 0.36 0.34 0.92
GCIY 0.55 Link 0.86 0.47 0.26
IM95 0.55 Link 0.32 0.29 0.99
TGBC11TKB 0.36 Link 0.32 0.05 0.97
FU97 0.34 Link 0.08 0.31 0.94
HGC27 0.09 Link 0.56 0.09 0.10
STS0421 0.04 NA 0.10 0.21 0.26

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.