Link has changed to https://portal.gdc.cancer.gov/projects/TCGA-BRCA
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anna.bernasconi •
How can i mean tags of TCGA (The Cancer Genome Atlas) Database?
Hi,
I work with TCGA (The Cancer Genome Atlas) database and I have downloaded mRNA gene expression microarray data concerning Breast Invasive Carcinoma disease. Subsets of the disease have been separated by tags, but i don't know the meaning of these tags. How can i mean these labels? For example, in Breast Cancer, there are 8 subsets for the disease (4 stages (I, II, III, IV) and 4 subtypes (Her2, Luminal A, Luminal B, Triple Negative)). Gene expression data for these eight subsets and normal subset have been given in a number of columns, so that the rows are gene names (17814 genes). There are 587 columns (samples) in this matrix that each column belongs to one of nine subsets (4 stages, 4 subtypes, 1 normal state). Top of each column exist a label, for example, TCGA-A1-A0SD-01A-11R-A115-07. What is this? I want to separate all columns related to Her2 state. How can i do this task? Please guide me.Thanks in advance!
1 answer
The TCGA barcode only shows the tumor type, not the stage. You need the clinical metadata associated with those datasets to get the disease subtype for each sample. If you go to https://gdc-portal.nci.nih.gov/projects/TCGA-BRCA there is a link/button for "Download Clinical" It will get you everything in json format and you can extract the disease stage.
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See this wiki page for explanation of the TCGA sample names: https://wiki.nci.nih.gov/display/TCGA/Understanding+TCGA+Biospecimen+IDs or https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode
Thank you, there are general information about TCGA sample names in this page: https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode
TCGA Code Table has separated the samples only by the Primary Solid Tumor and metastatic and Solid Tissue Normal in breast cancer disease, but i need to separate the samples according to each stags (I, II, III, IV) and each subtypes (Her2, Luminal A, Luminal B, Triple Negative). I can't do it.