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). <strong>TCGA-COAD.GDC_phenotype.tsv</strong> dataset: phenotype - Phenotype cohortGDC TCGA Colon Cancer (COAD)<br> dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv<br> downloadhttps://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv.gz; Full metadata<br> samples570<br> version11-27-2017<br> hubhttps://gdc.xenahubs.net<br> type of dataphenotype<br> authorGenomic Data Commons<br> raw datahttps://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90<br> raw datahttps://api.gdc.cancer.gov/data/<br> input data formatROWs (samples) x COLUMNs (identifiers) (i.e. clinicalMatrix)<br> 570 samples X 151 identifiersAll IdentifiersAll Samples <strong>TCGA-COAD.htseq_fpkm-uq.tsv</strong> dataset: gene expression RNAseq - HTSeq - FPKM-UQ cohortGDC TCGA Colon Cancer (COAD)<br> dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv<br> downloadhttps://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv.gz; Full metadata<br> samples512<br> version09-14-2017<br> hubhttps://gdc.xenahubs.net<br> type of datagene expression RNAseq<br> unitlog2(fpkm-uq+1)<br> platformIllumina<br> ID/Gene Mappinghttps://gdc.xenahubs.net/download/probeMaps/gencode.v22.annotation.gene.probeMap.gz; Full metadata<br> authorGenomic Data Commons<br> raw datahttps://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-80<br> raw datahttps://api.gdc.cancer.gov/data/<br> 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.<br> input data formatROWs (identifiers) x COLUMNs (samples) (i.e. genomicMatrix)<br> 60,484 identifiers X 512 samples