cBioPortal Nitish Mishra 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 threeyear pilot project begun in ID: 933536
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Slide1
The Cancer Genome Atlas (TCGA) and cBioPortal
Nitish
Mishra
Slide2TCGA 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)
Slide3Number of publications by using TCGA
Slide4Slide5Slide6Webserver 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)
Slide7TCGAbiolinks (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
R packages for TCGA data analysis