Alternative Db For Gene Expression Atlas

Question

[Assa Yeroslaviz]

Hi,

does anyone know about an alternative for the gene expression atlas from ebi?

We are interested in a database to save our bioinformatics results from different sources. We would like to combine analysis results from microarrays, NGS analysis, proteomics, ..., both from our experiments as well as from possible public data.

Is there any database like that out there?

I have looked into the gene expression atlas, which looks like a good thing and if I understand it correctly it is even downloadable. The problem is that it needs Oracle (11g+).

We are looking for something similar, but without the Oracle.

Thanks, Assa

Answer 1

[Malachi Griffith]

One strategy might be to create a local instance of the UCSC genome browser. Or an Ensembl local install. Projects, like Encode are faced with a similar need to store, access, and integrate disparate data types. They use UCSC for visualization and data mining. Another option is to create your own instance of Galaxy.

There may be some that are more specific to expression analysis, but given the types of data you are looking to handle you might be better off to stick with a relatively generic system with a large user base and all the benefits that go along with having an activity community addressing similar problems.