{"longTitle":"TCGA ovarian serous cystadenocarcinoma (OV) gene expression by RNAseq (polyA+ IlluminaHiSeq BC)","cohort":"TCGA Ovarian Cancer (OV)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ov/cgcc/bcgsc.ca/illuminahiseq_rnaseq/rnaseq/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"gene expression RNAseq","security":"public","rnatype":"polyA+","label":"IlluminaHiSeq BC","tags":["cancer"],"path":"data/public/TCGA/OV/HiSeq","anatomical_origin":["Ovary"],"name":"TCGA.OV.sampleMap/HiSeq","dataproducer":"British Columbia Cancer Agency TCGA genome characterization center","wrangling_procedure":"Level_3 data (file names: *.gene.quantification.txt) are downloaded from TCGA DCC, log2(x+1) transformed, and processed at UCSC into Xena repository.","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA ovarian serous cystadenocarcinoma","type":"genomicMatrix","wrangler":"Xena TCGAscript RNAseq processed on 2017-10-13","version":"2017-10-13","gdata_tags":["transcription"],"unit":"log2(RPKM+1)","notes":"the probeMap is hugo for the short term, however probably around 10% of the gene symbols are not HUGO names, but ENTRE genes","primary_disease":"ovarian serous cystadenocarcinoma","platform":"IlluminaHiSeq_RNASeq","colnormalization":true,"description":"The gene expression profile was measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the British Columbia Cancer Agency TCGA genome characterization center. Level 3 data was downloaded from TCGA data coordination center. This dataset shows the gene-level transcription estimates, as in RPKM values (Reads Per Kilobase of exon model per Million mapped reads). Genes are mapped onto the human genome coordinates using UCSC Xena HUGO probeMap (see ID/Gene mapping link below for details).<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>"}