get GTEx mean expression by tissue
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5.1 years ago
shaban.hiba8 ▴ 10

I've downloaded the GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.gct file from GTEx (https://gtexportal.org/home/datasets) and would like to calculate the mean expression per tissue type, but I can't seem to find documentation on which GTEx ID's belong to each tissue type.

For example the file contains a header that has GTEx IDs that look like this: GTEX-1117F-0226-SM-5GZZ7 or GTEX-111CU-1826-SM-5GZYN. which tissue type do these IDs belong to? Is there documentation on the website on this that I can't seem to find?

GTEx RNAseq RNA-Seq GTEx RNAseq • 3.3k views
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Use the histology viewer to find the tissue type:

https://gtexportal.org/home/histologyPage

0226 for subject GTEX-1117F is Adipose - Subcutaneous 1826 for subject GTEX-111CU is the same

You can download the data for ID to Tissue type from that page too.

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Thanks! If you write it as an answer I will accept it

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5.0 years ago
Oliver Slay ▴ 60

Use the GTEx Portal histology viewer to find the tissue type (and view the great histology slides):

https://gtexportal.org/home/histologyPage

In the table below you can filter by sample ID, scroll through or download the table in CSV format. If you click on one of the samples, you can view the histology slide below (zoom in and out). This page only contains the PAXgene samples (not the frozen brain samples - I've not found histology slides for GTEx Brain RoI anywhere, yet).

Alternatively, you can download a list (the RunInfo Table) from the NCBI SRA Run Selector - including the body site for each sample (and including brain regions):

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=GTEX&go=go#

The numbering for each subject appears to increment in the following way - possibly they were labelled as they were received:

GTEX-1117F-0126 Skin Exposed
GTEX-1117F-0226 Adipose (subcutaneous)
GTEX-1117F-0326 Nerve tibial...

but the last 4 numbers don't match between subjects:

GTEX-111CU-0126 Adrenal gland
GTEX-111CU-0226 Thyroid
GTEX-111CU-0326 Lung ...

0226 for subject GTEX-1117F is Adipose - Subcutaneous
1826 for subject GTEX-111CU is the same

The frozen brain regions are all numbered 0011 followed by the region number R1-R11 then A or B:

GTEX-WHSE-0011-R1A Hippocampus
GTEX-WHSE-0011-R1B Hippocampus
GTEX-WHSE-0011-R2A Substantia nigra
GTEX-WHSE-0011-R11A Cerebellar hemisphere

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5.1 years ago
husensofteng ▴ 410

You could use this file instead, it has the tissue names in the header:

Gene expression (TPM ) median per tissue type, note it is median not mean!

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I would but I also need to calculate standard deviation, so it's gotta be from the original GTEx counts

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