How to extract expression data for a specific gene from arrayExpress?
2
0
Entering edit mode
6.4 years ago

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!

arrayexpress microarray python R • 2.0k views
ADD COMMENT
0
Entering edit mode
6.4 years ago
5utr ▴ 370

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. 

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
3.3 years ago
j.salys • 0

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

ADD COMMENT

Login before adding your answer.

Traffic: 1674 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6