Dear all,

I want to find differential expressed miRNAs between tumor and normal tissues in TCGA data sets.

However when I download whole miRNA transcriptomic data sets, the number of samples belong to adjacent normal tissues or healthy individuals was extremely low(52 tumor samples against only 3 normal samples for Asians, for example).

I want to know if I have downloaded the miRNA data sets correctly.

Looking forward your advice

Nazanin


Yes, you have most likely downloaded them correctly. For RNA-seq and micro-RNA-seq, the number of normals that were sequenced was minimal. For some of the TCGA cancers, there were no (zero) normals profiled for gene expression.  One thing to remember is that most of the 'normal' samples are just from the tissue surrounding the primary tumour, so, they are not representative of true normal tissue.

The TCGA dataset that has most matched Tumour-Normal is breast cancer (BRCA), with ~108 pairings.

You may have to look for other public data if you want to increase your number of normals.

Kevin