SK-OV-3, A2780, OVCAR-3, IGROV-1, and PA-1 are some of the most widely used cell lines for ovarian 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 ovarian cancer cell lines with differences between the ovarian cancer cell lines SK-OV-3 vs A2780; SK-OV-3 vs OVCAR-3; SK-OV-3 vs IGROV-1; 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 Ovarian Cancer Cell Lines

The figure shows the presence of alterations for genes (TP53, PIK3CA, AKT1, BRCA1, PTEN, etc.) commonly associated with ovarian cancer in the cell lines: SKOV3, OVCAR4, IGROV1, EFO27, OV90, 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 ovarian cancer cell lines are shown to ensure a readable figure. Alterations for additional ovarian cancer cell lines and genes are available on cBioPortal using links on the table below.

Comparing ovarian 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 ovarian 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 Ovarian 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 ovarian cancer cell lines is available on cBioPortal using links on the table below.

The table shows ovarian 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
KURAMOCHI 1.00 Link 0.77 1.00 1.00
OAW28 1.00 Link 0.97 0.91 1.00
OVCAR4 0.99 Link 0.97 0.76 0.99
PEO1 0.99 NA 0.80 0.85 0.99
FUOV1 0.98 Link 0.97 0.85 0.75
JHOS4 0.98 Link 0.97 0.60 0.99
OVKATE 0.91 Link 0.63 0.62 1.00
OVCAR3 0.88 NA 0.85 0.34 0.99
OVMIU 0.87 NA 0.34 0.85 0.96
OV17R 0.85 NA 0.80 0.34 1.00
OVISE 0.85 Link 0.29 0.93 0.92
JHOS3 0.81 NA 0.05 0.99 0.99
OAW42 0.79 Link 0.28 0.89 0.84
ES2 0.78 Link 0.65 0.91 0.40
JHOS2 0.76 Link 0.05 0.91 0.99
HEY 0.74 NA 0.35 0.99 0.56
EFO21 0.73 Link 0.18 0.80 0.92
OVCAR8 0.70 Link 0.26 0.72 0.84
OV7 0.63 Link 0.49 0.89 0.32
OV56 0.61 Link 0.45 0.97 0.25
TOV112D 0.61 Link 0.69 0.23 0.75
A2780 0.54 Link 0.28 0.53 0.75
OVCA420 0.50 NA 0.67 0.80 0.02
DOV13 0.46 NA 0.42 0.09 0.94
IGROV1 0.46 Link 0.39 0.30 0.75
OC314 0.46 Link 0.39 0.14 0.92
OV90 0.46 Link 0.68 0.67 0.10
OVCAR5 0.46 NA 0.35 0.94 0.14
EFO27 0.44 Link 0.42 0.08 0.90
PA1 0.44 NA 0.32 0.14 0.94
CAOV4 0.42 Link 0.05 0.33 1.00
SKOV3 0.41 Link 0.54 0.12 0.70
RMGI 0.29 Link 0.05 0.36 0.75
OVTOKO 0.18 Link 0.26 0.10 0.56
TYKNU 0.15 Link 0.43 0.19 0.25
TOV21G 0.13 Link 0.34 0.10 0.40
OVK18 0.12 Link 0.40 0.09 0.32

Cell Lines with Common Mutations Found in TCGA Ovarian Cancer

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

Alterations

TP53 R175H (TCGA Altered: 3.8%; 15 out of 398 samples)

  • HS571T
  • TOV112D
  • TYKNU

TP53 R248Q (TCGA Altered: 2.5%; 10 out of 398 samples)

  • NIHOVCAR3
  • ONCODG1

TP53 R273C (TCGA Altered: 1.3%; 5 out of 398 samples)

  • EFO27

TP53 R273H (TCGA Altered: 2.3%; 9 out of 398 samples)

  • OC314
  • OC316

TP53 R282W (TCGA Altered: 1%; 4 out of 398 samples)

  • OVKATE

TP53 S241F (TCGA Altered: 1.5%; 6 out of 398 samples)

  • ES2

TP53 Y220C (TCGA Altered: 2.3%; 9 out of 398 samples)

  • COV362

KRAS G12V (TCGA Altered: 1%; 4 out of 398 samples)

  • OVCAR5

PIK3CA H1047R (TCGA Altered: 0.5%; 2 out of 398 samples)

  • MCAS
  • SKOV3
  • SNU840

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.