Question: Gene expression data in Human Pancreatic Beta Cells
0
gravatar for Natasha
6 months ago by
Natasha30
Natasha30 wrote:

Hello,

I’m trying to access the gene expression data of the enzymes catalyzing the metabolic pathways from studies on the pancreatic islets of diabetic subjects (for example, the gene expression level reported in control vs. diabetic in http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011499#s4. Are there specific databases from which such gene expression data can be accessed?

Any help would be highly appreciated.

gene expression gene • 330 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe37k • written 6 months ago by Natasha30

That helped a lot. I wish to get an average value of gene expression for a specific list of genes. For instance, in the study with GEO accession ID -GSE15543(first hit from the search with keywords,(Pancreatic Beta Cells) AND "Homo sapiens"[porgn:__txid9606]) 33 samples are listed. After defining data sets, I'm able to see the distribution of the gene expression.

Is there a way to programmatically compute the average value of gene expression, for a specific list of genes, from all the 33 samples?

ADD REPLYlink written 6 months ago by Natasha30

Sure, but in which format is your data, currently?

ADD REPLYlink written 6 months ago by Kevin Blighe37k

I'm using the profile graph option in GEO2R (example) to view the expression data. While I was looking for the downloadable file formats, I came across soft file format.

I'm new to all of this, I would like to know the recommended format that one can use to parse the expression data easily.

ADD REPLYlink written 6 months ago by Natasha30

In the link that you provide, the easiest thing to do is to go to the R script tab and then run the code there. This will then give you the normalised log2 expression data, on which you can then instantly perform downstream analyses.

ADD REPLYlink written 5 months ago by Kevin Blighe37k
1
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

Have you looked on the Gene Expression Omnibus (GEO)? Go HERE and search for:

(Pancreatic Beta Cells) AND "Homo sapiens"[porgn:__txid9606]

Kevin

ADD COMMENTlink modified 5 months ago • written 6 months ago by Kevin Blighe37k

Is it possible to add one more filter to this search? For instance, I wish to download the data from studies relevant to Diabetes.

ADD REPLYlink written 6 months ago by Natasha30

Yes, please refer to the updated answer to your new question, here: A: Gene expression data from GEO

ADD REPLYlink written 5 months ago by Kevin Blighe37k
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