BxPC-3, AsPC-1, HPAF-II, CFPAC-1, and SW1990 are some of the most widely used cell lines for pancreatic 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 pancreatic cancer cell lines with differences between the pancreatic cancer cell lines BxPC-3 vs AsPC-1; BxPC-3 vs HPAF-II; BxPC-3 vs CFPAC-1; and etc.
If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.
The figure shows the presence of alterations for genes (KRAS, TP53, SMAD4, CDKN2A, GNAS, etc.) commonly associated with pancreatic cancer in the cell lines: YAPC, ASPC1, CFPAC1, PSN1, KP2, 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 pancreatic cancer cell lines are shown to ensure a readable figure. Alterations for additional pancreatic cancer cell lines and genes are available on cBioPortal using links on the table below.
Comparing pancreatic 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
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 pancreatic cancer cell lines is available on cBioPortal using links on the table below.
Cell Line | % Rank by Avg % Ranks | More Line Info | % Rank by Mutation | % Rank by Copy Number | % Rank by Expression |
---|---|---|---|---|---|
KP2 | 1.00 | Link | 0.99 | 0.96 | 0.90 |
SU8686 | 1.00 | Link | 0.99 | 0.92 | 0.95 |
YAPC | 1.00 | Link | 0.99 | 0.94 | 0.92 |
HUPT3 | 0.99 | Link | 0.86 | 0.89 | 0.97 |
CAPAN1 | 0.98 | Link | 0.99 | 0.59 | 1.00 |
PANC0327 | 0.98 | Link | 0.92 | 0.67 | 0.97 |
ASPC1 | 0.97 | Link | 0.56 | 0.89 | 0.97 |
PANC0403 | 0.97 | Link | 0.85 | 0.67 | 0.97 |
PANC0813 | 0.97 | Link | 0.55 | 0.89 | 0.99 |
SW1990 | 0.97 | Link | 0.86 | 0.61 | 0.98 |
PANC0203 | 0.96 | Link | 0.66 | 0.73 | 0.98 |
PL4 | 0.96 | NA | 0.99 | 0.43 | 0.97 |
PSN1 | 0.94 | Link | 0.86 | 0.73 | 0.71 |
BXPC3 | 0.91 | Link | 0.62 | 0.71 | 0.90 |
CFPAC1 | 0.91 | Link | 0.99 | 0.24 | 1.00 |
HUPT4 | 0.90 | Link | 0.74 | 0.45 | 0.99 |
DANG | 0.89 | Link | 0.92 | 0.36 | 0.88 |
HPAC | 0.89 | Link | 0.45 | 0.71 | 0.99 |
PANC1005 | 0.89 | Link | 0.48 | 0.89 | 0.80 |
HPAFII | 0.86 | Link | 0.55 | 0.56 | 1.00 |
PATU8902 | 0.82 | Link | 0.85 | 0.30 | 0.86 |
CAPAN2 | 0.73 | Link | 0.42 | 0.43 | 0.98 |
MIAPACA2 | 0.71 | Link | 0.98 | 0.45 | 0.35 |
MZ1PC | 0.71 | NA | 0.53 | 0.28 | 0.98 |
KP1N | 0.69 | NA | 1.00 | 0.59 | 0.19 |
KP4 | 0.69 | Link | 1.00 | 0.36 | 0.40 |
PL18 | 0.67 | NA | 0.59 | 0.47 | 0.68 |
KP3 | 0.63 | Link | 0.52 | 0.43 | 0.74 |
SUIT2 | 0.56 | Link | 0.53 | 0.09 | 0.96 |
PATU8988T | 0.43 | Link | 1.00 | 0.34 | 0.08 |
Alterations present in cell lines also present in at least two TCGA Pan-Cancer Atlas (PAAD) samples on cBioPortal.
Each project has unique questions. TumorComparer (tumorcomparer.org) facilities customized comparisons of cell line datasets to tumor samples directly from the browser.
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.