Historical NCI Genomic Data Commons data (09-14-2017)

Historical NCI Genomic Data Commons data (v09-14-2017). Clinical ('phenotype') and gene expression (HTSeq FPKM-UQ).

TCGA-COAD.GDC_phenotype.tsv

dataset: phenotype - Phenotype

cohortGDC TCGA Colon Cancer (COAD)
dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv
downloadhttps://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv.gz; Full metadata
samples570
version11-27-2017
hubhttps://gdc.xenahubs.net
type of dataphenotype
authorGenomic Data Commons
raw datahttps://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90
raw datahttps://api.gdc.cancer.gov/data/
input data formatROWs (samples) x COLUMNs (identifiers) (i.e. clinicalMatrix)
570 samples X 151 identifiersAll IdentifiersAll Samples

TCGA-COAD.htseq_fpkm-uq.tsv

dataset: gene expression RNAseq - HTSeq - FPKM-UQ

cohortGDC TCGA Colon Cancer (COAD)
dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv
downloadhttps://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv.gz; Full metadata
samples512
version09-14-2017
hubhttps://gdc.xenahubs.net
type of datagene expression RNAseq
unitlog2(fpkm-uq+1)
platformIllumina
ID/Gene Mappinghttps://gdc.xenahubs.net/download/probeMaps/gencode.v22.annotation.gene.probeMap.gz; Full metadata
authorGenomic Data Commons
raw datahttps://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-80
raw datahttps://api.gdc.cancer.gov/data/
wranglingData from the same sample but from different vials/portions/analytes/aliquotes is averaged; data from different samples is combined into genomicMatrix; all data is then log2(x+1) transformed.
input data formatROWs (identifiers) x COLUMNs (samples) (i.e. genomicMatrix)
60,484 identifiers X 512 samples