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Protocols

TCGA Data Portal specifications

Information


Unique identifier OMICS_02593
Name TCGA Data Portal
Alternative names The Cancer Genome Atlas Data Portal, TCGA, The Cancer Genome Atlas
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline TCGA Data Portal

Publications for The Cancer Genome Atlas Data Portal

TCGA Data Portal citations

 (2330)
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Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

2018
Nat Commun
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w
call_split See protocol

[…] In order to deal with the level of ‘sparsity’ of the gene expression matrix and with the specific type of signal of TCGA RNA-Seq data, a number of gene expression rows were trimmed from the expression spreadsheet of LUSC patients before running a gene-set based analysis; this pre-processing step prevents the inflat […]

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Molecular and clinical characterization of PTPN2 expression from RNA seq data of 996 brain gliomas

2018
PMCID: 5953404
PMID: 29764444
DOI: 10.1186/s12974-018-1187-4
call_split See protocol

[…] istics and whole genome RNA-seq data of 325 patients with glioma (World Health Organization (WHO) grades II–IV) from the CGGA dataset, have been described in our previous study []. Besides, data from TCGA were downloaded from the cBioPortal (http://www.cbioportal.org/), and 671 gliomas (WHO grades II–IV) were analyzed in this study. […]

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STT3 dependent PD L1 accumulation on cancer stem cells promotes immune evasion

2018
Nat Commun
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6
call_split See protocol

[…] The mRNA expression (RNA Seq V2 RSEM) database of TCGA Breast Invasive Carcinoma (n = 1100) was downloaded from the open-source resource of the cBioPortal for Cancer Genomics [http://www.cbioportal.org/index.do]. The log2 ratio of downloaded data was […]

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Aurora kinase A (AURKA) interaction with Wnt and Ras MAPK signalling pathways in colorectal cancer

2018
Sci Rep
PMCID: 5951826
PMID: 29760449
DOI: 10.1038/s41598-018-24982-z

[…] To compare the effect of AURKA on Wnt and Ras-MAPK signalling in CRC tissue data to our CRC cell line results we analysed the TCGA COADREAD RNA-seq and somatic copy number aberration data for 330 microsatellite stable tumour samples retrieved from Firehose (March 2017). First, the samples were labelled by AURKA-gain and AURK […]

library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] are (Interactive Software, Rouen, France), which contains the algorithms SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder, ESE-Finder, and RESCUE-ESE. Mutation data from all TCGA series were retrieved from the GDC portal in day 29th of September 2017. Frequencies of germline mutations in general population were retrieved from the ExAC database (access on 12 October 2017). […]

library_books

The lncRNA myocardial infarction associated transcript centric competing endogenous RNA network in non small cell lung cancer

2018
PMCID: 5958945
DOI: 10.2147/CMAR.S163395

[…] The RNA and miRNA expression data (level 3) and the corresponding clinical information of NSCLC patients were retrieved from TCGA database portal (https://tcga-data.nci.nih.gov/tcga/). Both RNA-seq data and miRNA-seq data of tumor tissues and adjacent non-tumor tissues were included, according to the histologic staging data […]

Citations

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TCGA Data Portal institution(s)
Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Research Administration Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

TCGA Data Portal review

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Anonymous user #33015

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Dataset
Good tool. help about genomic anaysis