How to extract expression data for a specific gene from arrayExpress?

Question

[abhishekniroula7]

Hi,

I am interested to find the expression pattern of a specific gene of interest through different datasets in arrayExpress for example in different cancers. Looking for all the datasets and looking into the datasets is too much work. Is there an easier way to do this? Anybody could direct me to some useful information in this direction?

Thanks!

Answer 1

[5utr]

I don't know how get that from arrayExpress but most of the datasets on arrayExpress are also on GEO (Gene Expression Omnibus). On GEO you can access the gene profiles directly http://www.ncbi.nlm.nih.gov/geoprofiles and download the expression data for that particular gene.

[abhishekniroula7]

Hi @Gian

Thank you for pointing to GEO profiles. I tried GEO profiles while I was waiting for answer to this question. It is very useful. I searched for data using gene name and then filtered the hits using other criteria. But, the data from different studies are incomparable.

Let's see if we find more interesting tool or if somebody would like to make a tool to integrate the data.

Answer 2

[j.salys]

You can use Python to analyze GEO data. Check this post: http://friendlypython.herokuapp.com/2018/6/analysis-geogene-expression-omnibus-data/