Question: Where do I find the label, whether this file data corroborates to a healthy tissue or a cancerous one in tcga data?
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gravatar for acc.inpro321
2.9 years ago by
acc.inpro32130
acc.inpro32130 wrote:

I downloaded the TCGA dataset for LUAD (Lung Cancer), I find each file with miRNA sequence data like readCount and parts per million value and their are around 123 samples. But where do I find the label, whether this sample is cancerous or not?

Sample Files

TCGA-05-4244-01A-01T-1108-13.hg19.mirbase20.mirna.quantification.txt TCGA-05-4244-01A-01T-1108-13.mirna.quantification.txt TCGA-05-4249-01A-01T-1108-13.hg19.mirbase20.mirna.quantification.txt TCGA-05-4249-01A-01T-1108-13.mirna.quantification.txt

  1. What is the difference in between isoform and mirna?
  2. What is the difference in between hg19.mirbase20.mirna and mirna? Should I include both files in my training model?
  3. Where do I find the label, whether this file data corroborates to a healthy tissue or a cancerous one?
microrna-seq tcga • 893 views
ADD COMMENTlink modified 2.9 years ago by Khader Shameer18k • written 2.9 years ago by acc.inpro32130
0
gravatar for Khader Shameer
2.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

To compile clinical phenotypes including case or control, tumor-grade, pathology report etc., you can use one of the secondary databases like CBioPortal or Harnomonizome

  1. To understand the difference between isoform and mirna, Wikipedia articles are good start
  2. hg19.mirbase20.mirna = mapped to hg19; mirna = could be the same or annotations using a different refernce database
  3. You can get the full summary including clinical phenome data here. One of your sample is case (patient with primary tumor) and other is a control; this classification could change based on your case-control criteria)

PS. Not sure from where you downloaded the TCGA data.

ADD COMMENTlink written 2.9 years ago by Khader Shameer18k

Hello Sir, I downloaded the data, but I am not able to find any normal matched sample, then how should I train my algorithm; could you please suggest some other sites to get miRNA data from; both cancer samples and tumor samples. Thanks in advance!

ADD REPLYlink written 2.9 years ago by acc.inpro32130

Here you go: How To Retrieve Tcga Mirna-Mrna Data

ADD REPLYlink written 2.9 years ago by Khader Shameer18k
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