Exploring cancer genomic data from the cancer genome atlas project

  • Lee, Ju-Seog (Department of Systems Biology, The University of Texas MD Anderson Cancer Center)
  • Received : 2016.08.16
  • Published : 2016.11.30


The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis of cancer development. Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways. To take advantage of the advancement, it will be necessary to learn systematic approaches that can help to uncover novel genes reflecting genetic alterations, prognosis, or response to treatments. This minireview describes the updated status of TCGA project and explains how to use TCGA data.


Clinical significance;Genomics;Methylation;Proteomics;The cancer genome atlas


Supported by : National Institutes of Health


  1. Cerami E, Gao J, Dogrusoz U et al (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2, 401-404
  2. Goswami CP and Nakshatri H (2014) PROGgeneV2: enhancements on the existing database. BMC Cancer 14, 970
  3. Koch A, De Meyer T, Jeschke J and Van Criekinge W (2015) MEXPRESS: visualizing expression, DNA methyla-tion and clinical TCGA data. BMC Genomics 16, 636
  4. Li J, Lu Y, Akbani R et al (2013) TCPA: a resource for cancer functional proteomics data. Nat Methods 10, 1046-1047
  5. Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921
  6. Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291, 1304-1351
  7. DeNicola GM, Chen PH, Mullarky E et al (2015) NRF2 regulates serine biosynthesis in non-small cell lung cancer. Nat Genet 47, 1475-1481
  8. Park YY, Kim K, Kim SB et al (2012) Reconstruction of nuclear receptor network reveals that NR2E3 is a novel upstream regulator of ESR1 in breast cancer. EMBO Mol Med 4, 52-67
  9. Saha SK, Parachoniak CA, Ghanta KS et al (2014) Mutant IDH inhibits HNF-4alpha to block hepatocyte differentiation and promote biliary cancer. Nature 513, 110-114
  10. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068
  11. International Cancer Genome Consortium (2010) International network of cancer genome projects. Nature 464, 993-998
  12. Cancer Genome Atlas Research Network (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615
  13. Cancer Genome Atlas Research Network (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525
  14. Cancer Genome Atlas Research Network (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337
  15. Han L, Diao L, Yu S et al (2015) The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers. Cancer Cell 28, 515-528
  16. Yates LA, Norbury CJ and Gilbert RJ (2013) The long and short of microRNA. Cell 153, 516-519
  17. Spurrier B, Ramalingam S and Nishizuka S (2008) Reverse-phase protein lysate microarrays for cell signaling analysis. Nat Protoc 3, 1796-1808
  18. Gutman DA, Cobb J, Somanna D et al (2013) Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data. J Am Med Inform Assoc 20, 1091-1098
  19. Clark K, Vendt B, Smith K et al (2013) The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository. J Digit Imaging 26, 1045-1057
  20. Consortium IHGS (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931-945

Cited by

  1. What is the potential of nanolock– and nanocross–nanopore technology in cancer diagnosis? pp.1744-8352, 2017,
  2. Five Novel Oncogenic Signatures Could Be Utilized as AFP-Related Diagnostic Biomarkers for Hepatocellular Carcinoma Based on Next-Generation Sequencing vol.63, pp.4, 2018,
  3. Clinical significance of APOB inactivation in hepatocellular carcinoma vol.50, pp.11, 2018,
  4. A pan-cancer study of the transcriptional regulation of uricogenesis in human tumours: pathological and pharmacological correlates vol.38, pp.5, 2018,
  5. Silencing non-SMC chromosome-associated polypeptide G inhibits proliferation and induces apoptosis in hepatocellular carcinoma cells pp.1205-7541, 2018,
  6. Oncoyeasti: a web-based application to translate data obtained from Saccharomyces cerevisiae high-throughput drug screens into cancer therapeutics vol.7, pp.2046-1402, 2018,
  7. Clinical and genomic landscape of gastric cancer with a mesenchymal phenotype vol.9, pp.1, 2018,
  8. Multi-platform analysis of methylation-regulated genes in human lung adenocarcinoma vol.82, pp.1, 2019,