{"owner":"TCGA","longTitle":"TCGA thyroid carcinoma (THCA) gene expression by RNAseq (polyA+ IlluminaHiSeq percentile)","cohort":"TCGA Thyroid Cancer (THCA)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"gene expression RNAseq","security":"public","rnatype":"polyA+","label":"IlluminaHiSeq percentile","tags":["cancer"],"path":"data/public/TCGA/THCA/HiSeqV2_percentile","anatomical_origin":["Thyroid Gland"],"name":"TCGA.THCA.sampleMap/HiSeqV2_percentile","dataproducer":"University of North Carolina TCGA genome characterization center","wrangling_procedure":"Level_3 data (file names: *.rsem.genes.normalized_results) are downloaded from TCGA DCC, percentile ranked, and processed at UCSC into Xena repository.","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA thyroid carcinoma","type":"genomicMatrix","wrangler":"Xena TCGAscript RNAseq processed on 2017-10-13","version":"2017-10-13","gdata_tags":["transcription"],"unit":"percentile rank","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":"thyroid carcinoma","platform":"IlluminaHiSeq_RNASeqV2","colnormalization":true,"description":"For each sample, we rank genes RSEM values between 0% to 100%. This dataset is gene expression estimation in percentile rank, which higher value representing higher expression. The dataset can be used to compare this RNAseq data  with other cohorts when the other data is processed in the same way (i.e. percentile ranking). Genes are mapped onto the human genome coordinates using UCSC Xena HUGO 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/thca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_THCA.IlluminaHiSeq_RNASeqV2.Level_3.1.12.0/DESCRIPTION.txt\" target=\"_blank\"><u>DCC description</u></a><br><br>For comparing data within this cohort, we recommend to use the \"gene expression RNAseq\" dataset. For questions regarding the gene expression of this particular cohort in relation to other types tumors, you can use the pancan normalized version of the \"gene expression RNAseq\" data. For comparing with data outside TCGA, we recommend using the percentile version if the non-TCGA data is normalized by percentile ranking. For more information, please see our Data FAQ: <a href=https://docs.google.com/document/d/1q-7Tkzd7pci4Rz-_IswASRMRzYrbgx1FTTfAWOyHbmk/edit?usp=sharing target=\"_blank\"><u>here</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>"}