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

{"longTitle":"TCGA lung cancer (LUNG) segmented copy number (delete germline cnv)","cohort":"TCGA Lung Cancer (LUNG)","dataSubType":"copy number segments","security":"public","label":"After remove germline cnv","tags":["cancer","non-small cell lung cancer"],"anatomical_origin":["Lung"],"name":"TCGA.LUNG.sampleMap/SNP6_nocnv_genomicSegment","sample_type":["tumor"],"assembly":"hg19","type":"genomicSegment","version":"2017-09-08","unit":"log2(tumor/normal)","primary_disease":"lung cancer","description":"The dataset is combined from TCGA lung squamous cell carcinoma and lung adenocarcinoma datasets. TCGA lung cancer (LUNG) segmented copy number variation profile after removing common germline copy number variation.<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. A fixed set of common germline cnv probes were removed prior to segmentation. 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/lusc/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_LUSC.Genome_Wide_SNP_6.mage-tab.1.2015.0/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 lung cancer (LUNG) segmented copy number (delete germline cnv)

{"owner":"TCGA","longTitle":"TCGA lung cancer (LUNG) gene-level non-silent somatic mutation (pancan awg)","cohort":"TCGA Lung Cancer (LUNG)","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"PANCAN AWG","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUNG/mutation","anatomical_origin":["Lung"],"name":"TCGA.LUNG.sampleMap/mutation","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","version":"2017-09-08","unit":"binary non-silent mutation","primary_disease":"lung cancer","description":"The dataset is combined from TCGA lung squamous cell carcinoma and lung adenocarcinoma datasets. TCGA lung cancer (LUNG) somatic mutation data. Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>Somatic mutations calls (even on the same tumor DNA extract) are affected by many factors including library prep, sequencing process, read mapping method, reference genome used, genome annotation, calling algorithms, and ad-hoc pre/postprocessing such as black list genes, target selection regions, and black list samples. This dataset is the best effort made by the TCGA PANCANCER Analysis Working Group. Raw PANCAN mutation data can be downloaded at the url site shown below.<br><br>"}