Question: How can i mean tags of TCGA (The Cancer Genome Atlas) Database?
0
gravatar for leila
2.2 years ago by
leila 30
leila 30 wrote:

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!

ADD COMMENTlink modified 2.2 years ago by dyollluap300 • written 2.2 years ago by leila 30

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

ADD REPLYlink written 2.2 years ago by genomax64k

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by leila 30
0
gravatar for dyollluap
2.2 years ago by
dyollluap300
USA, California, Bay Area
dyollluap300 wrote:

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.

ADD COMMENTlink written 2.2 years ago by dyollluap300

Link has changed to https://portal.gdc.cancer.gov/projects/TCGA-BRCA

ADD REPLYlink written 7 days ago by anna.bernasconi0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1235 users visited in the last hour