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The Cancer Genome Atlas (TCGA) and cBioPortal

The Cancer Genome Atlas (TCGA) and cBioPortal. Nitish Mishra. TCGA history. TCGA is a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing.

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The Cancer Genome Atlas (TCGA) and cBioPortal

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  1. The Cancer Genome Atlas (TCGA) and cBioPortal Nitish Mishra

  2. TCGA history • TCGA is a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing. • TCGA is supervised by the Center for Cancer Genomics and the National Human Genome Research Institute. A three-year pilot project, begun in 2006, focused on characterization of three types of human cancers: glioblastoma, lung, and ovarian cancer. • In 2009, it expanded into phase II, which planned to complete the genomic characterization and sequence analysis of 20–25 different tumor types by 2014 • Gene expression (RNA-seq and array), copy number variation (array and genome sequencing), SNP genotyping (GGS and WES), DNA methylation (array and RBSS), microRNA profiling, proteomics (RPPA), and chromatin accessibility (ATAC-seq) • TCGA have published ~70 research articles. • There are 3554 authorized requesters associated with TCGA study (currently)

  3. Number of publications by using TCGA

  4. Webserver based on TCGA • https://www.cbioportal.org/ (cBioPortal) • http://gepia.cancer-pku.cn/ (GEPIA) • https://biit.cs.ut.ee/methsurv/ (MethSurv) • https://hgserver1.amc.nl/cgi-bin/r2/main.cgi (R2 gene) • https://xenabrowser.net/datapages/ (Xena) • https://www.proteinatlas.org/ (The Human Protein Atlas) • https://cptac-data-portal.georgetown.edu/cptacPublic/ (CPTAC)

  5. R packages for TCGA data analysis • TCGAbiolinks (https://github.com/BioinformaticsFMRP/TCGAbiolinks) • RTCGAToolbox (https://github.com/mksamur/RTCGAToolbox) • GenomicDataCommons (https://github.com/Bioconductor/GenomicDataCommons) • GDCRNATools (https://github.com/Jialab-UCR/GDCRNATools) • cgdsr (https://github.com/cBioPortal/cgdsr) cBioPortal

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