TCGA lung cancer (LUNG) exon expression by RNAseq (polyA+ IlluminaHiSeq)

{"owner":"TCGA","longTitle":"TCGA lung cancer (LUNG) gene expression (AgilentG4502A_07_3 array)","cohort":"TCGA Lung Cancer (LUNG)","dataSubType":"gene expression array","security":"public","label":"AgilentG4502A_07_3","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUNG/AgilentG4502A_07_3","anatomical_origin":["Lung"],"name":"TCGA.LUNG.sampleMap/AgilentG4502A_07_3","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","version":"2017-09-08","gdata_tags":["transcription"],"unit":"normalized Agilent array expression","primary_disease":"lung cancer","colnormalization":true,"description":"The dataset is combined from TCGA lung squamous cell carcinoma and lung adenocarcinoma datasets. TCGA lung cancer (LUNG) gene expression data by agilent array.<br><br> The gene expression profile was measured experimentally using Agilent 244K custom gene expression G4502A_07_3 microarrays by the University of North Carolina TCGA genomic characterization center.  Level 3 interpreted level data was downloaded from TCGA data coordination center. This dataset shows the gene level transcription estimates (level 3 data), as in log2 lowess normalized ratio of sample signal to reference signal (cy5/cy3) collapsed by gene. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap.<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>"}

TCGA lung cancer (LUNG) gene expression (AgilentG4502A_07_3 array)

TCGA lung squamous cell carcinoma (LUSC) DNA methylation (HumanMethylation27)

TCGA lung squamous cell carcinoma (LUSC) DNA methylation (HumanMethylation450)

{"longTitle":"TCGA lung squamous cell carcinoma (LUSC) copy number gistic2 estimate","cohort":"TCGA Lung Squamous Cell Carcinoma (LUSC)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/LUSC/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUSC/Gistic2_CopyNumber_Gistic2_all_data_by_genes","anatomical_origin":["Lung"],"name":"TCGA.LUSC.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into xena repository","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA lung squamous cell carcinoma","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"Gistic2 copy number","primary_disease":"lung squamous cell carcinoma","description":"TCGA lung squamous cell carcinoma (LUSC) gene-level copy number variation (CNV) estimated using the GISTIC2 method.<br><br> Copy number profile was measured experimentally using whole genome microarray at a TCGA genome characterization center. Subsequently, TCGA FIREHOSE pipeline applied GISTIC2 method to produce segmented CNV data, which was then mapped to genes to produce gene-level estimates. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}