TCGA colon & rectum adenocarcinoma (COADREAD) copy number gistic2 thresholded estimate

{"longTitle":"TCGA colon & rectum adenocarcinoma (COADREAD) segmented copy number","cohort":"TCGA Colon and Rectal Cancer (COADREAD)","dataSubType":"copy number segments","security":"public","label":"Before remove germline cnv","tags":["cancer"],"path":"data/public/TCGA/COADREAD/SNP6_genomicSegment","anatomical_origin":["Colon and Rectum"],"name":"TCGA.COADREAD.sampleMap/SNP6_genomicSegment","sample_type":["tumor"],"assembly":"hg19","type":"genomicSegment","version":"2017-09-08","unit":"log2(tumor/normal)","primary_disease":"colon & rectum adenocarcinoma","description":"The dataset is combined from TCGA colon adenocarcinoma and rectum adenocarcinoma datasets. TCGA colon & rectum adenocarcinoma (COADREAD) segmented copy number variation profile.<br><br> Copy number profile was measured experimentally using the Affymetrix Genome-Wide Human SNP Array 6.0 platform at the Broad TCGA genome characterization center. Raw copy numbers were estimated at each of the SNP and copy-number markers. <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/15475419\" target=\"_blank\"><u>Circular binary segmentation</u></a> was then used to segment the copy number data. Segments are mapped to hg19 genome assembly at Broad. Reference to the algorithm used by Broad to produce the dataset: <a href =\"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_COAD.Genome_Wide_SNP_6.mage-tab.1.2010.0/DESCRIPTION.txt\" target=\"_blank\"> <u>DCC description</u></a> and <a href=\"http://www.nature.com/nature/journal/vaop/ncurrent/suppinfo/nature07385.html\" target=\"_blank\"><u>nature 2008</u></a> .<br><br>"}

TCGA colon & rectum adenocarcinoma (COADREAD) segmented copy number

{"owner":"TCGA","longTitle":"TCGA colon & rectum adenocarcinoma (COADREAD) exon expression by RNAseq (polyA+ IlluminaHiSeq)","cohort":"TCGA Colon and Rectal Cancer (COADREAD)","probeMap":"unc_v2_exon_hg19_probe_TCGA","dataSubType":"exon expression RNAseq","security":"public","label":"IlluminaHiSeq","tags":["cancer"],"path":"data/public/TCGA/COADREAD/HiSeqV2_exon","anatomical_origin":["Colon and Rectum"],"name":"TCGA.COADREAD.sampleMap/HiSeqV2_exon","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","version":"2017-09-08","gdata_tags":["transcription"],"unit":"log2(RPKM+1)","primary_disease":"colon & rectum adenocarcinoma","colnormalization":true,"description":"The dataset is combined from TCGA colon adenocarcinoma and rectum adenocarcinoma datasets.  The exon expression profile was measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the University of North Carolina TCGA genome characterization center. Level 3 data was downloaded from TCGA data coordination center. This dataset shows the exon-level transcription estimates, as in RPKM values (Reads Per Kilobase of exon model per Million mapped reads). Exons are mapped onto the human genome coordinates using UCSC Xena unc_RNAseq_exon probeMap (see ID/Gene mapping link below for details. Reference to method description from University of North Carolina TCGA genome characterization center: <a href=\"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_COAD.IlluminaHiSeq_RNASeqV2.Level_3.1.12.0/DESCRIPTION.txt\" target=\"_blank\"><u>DCC description</u></a><br><br>In order to more easily view the differential expression between samples, we set the default view to center each gene or exon to zero by independently subtracting the mean of each gene or exon on the fly. Users can view the original non-normalized values by adjusting visualization settings.<br><br>"}