Available data types and smart analyses                 * See example analyses - video demos

Patient samples

Kaplan-Meier plots
(Survival analysis)
  • Somatic mutations
  • RNA expression
  • Protein expression and phosphorylation
  • Tumor infiltrating cells
Box or Scatter plots
(Cross-association)
  • Somatic mutations
  • RNA expression
  • Protein expression and phosphorylation
  • Tumor infiltrating cells
Box plots
(Normal-Tumor paired samples)
  • Comparative RNA expression

Cell lines

Box or Scatter plots
(Cross-association)
  • Mutations
  • RNA expression
  • Protein expression and phosphorylation
  • shRNA
  • CRISPR (sqRNA)
  • Drugs
Box plots and heatmaps
(Drug-induced RNA expression)
  • Comparative RNA expression before and after drug treatment

Number of data integrated into Q-omics software

Data set # Lineages # Samples # Entities Data type Source/Download
Cell line data RNA expression 20 1,061 19,137 RNA sequencing CCLE[1]/Depmap Expression 20Q1[2]
Protein expression and phosphorylation 20 899 214 Reverse Phase Protein Array Depmap/Protein Array[2]
Protein abundance 20 949 8,424 Mass spectrometry [11]
sgRNA 20 741 18,110 CRISPR Depmap/CRISPR 20Q1[2]
shRNA 20 587 16,800 RNAi shRNA Depmap/RNAi (Achilles + DRIVE + Marcotte, DEMETER2)[2]
Drug response 20 1,001 561 Drug response GDSC[3]/Depmap Sanger GDSC1 and GDSC2[2]
Mutations 20 1,281 18,731 Exome sequencing CCLE/Depmap Mutation 20Q1[2]
Drug-induced RNA expression 13 60 12,305 (genes)
15 (drugs)		 DNA microarray NCI60[4]/GSE116436[5]
Tissue data Tumor RNA expression 34 9,951 38,311 RNA sequencing TCGA[6], GENIE[7], CPTAC[12] /GDC portal[8]
Protein expression and phosphorylation 32 6,985 275 Reverse Phase Protein Array TCGA/GDC portal
Protein abundance and post-translational modification 10 1,067 >50,000 Mass spectrometry CPTAC/PDC portal[13]
Paired normal vs. tumor: RNA expression 18 679 38,311 RNA sequencing TCGA/GDC portal
Somatic mutations 34 9,100 20,850 Exome sequencing TCGA, GENIE/GDC portal
Infiltrating cells 33 8,954 64 (cell types) Cell type enrichment score xCell[9]/xCell portal[10]

References


  1.  Barretina et al., (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607.
  2. https://depmap.org/portal/download/
  3. Yang, et al., (2013) Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Research. 41 (Database issue): D955 - D961.
  4. Monks, et al. (2018) The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel. Cancer Res 78, 6807-6817.
  5. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116436
  6. Cancer Genome Atlas Research, N., et al. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet 45, 1113-1120.
  7. AACR Project GENIE Consortium, (2017) AACR Project GENIE: Powering Precision Medicine through an International Consortium. Cancer Discovery 7(8):818-831.
  8. https://portal.gdc.cancer.gov/
  9. Dvir A., Zicheng H. and Atul J.B. (2017) xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biology 18:220.
  10. https://xcell.ucsf.edu/
  11. Gonçalves, et al. (2022) Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40(8), 835-849.
  12. https://proteomics.cancer.gov/
  13. https://proteomic.datacommons.cancer.gov/pdc/