BioGPS, command line?

[sindrle]

Hi!
Just a question, I have seen some people using BioGPS to get a feel of where a certain gene is more/less expressed, in terms of tissues.

BioGPS only takes 10 inputs at a time and is a "point and click" - kind of application.

So, do any know of a similar software that is "high throughput"? I.e. checking 2000 differential expressed genes for those only highly expressed in say brain.


Thanks!

[gtsu]

Hi,
Not sure I understood what you're trying to do. If you want to just look at tons of genes (more than the 10 limit input), you can download the BioGPS datasets of interest at: http://biogps.org/downloads/ and then run your own queries.

[sindrle]

Lets say you want to search for highly expressed genes in a tissue that also is secreted, then its more likely you will find it i say blood plasma, since other tissues don't influence that much.

If you have a list of 2000 differentially expressed genes, it would be nice to subset the highest expressed ones (according to BioGPS) in one run. Not 10 at a time!

I will look into the files you linked, I don't see gene names, but Ill search around. Thanks!

[gtsu]

For gene names, because these are microarray datasets, the information is listed by the probes (there may be different probes against each gene). You can find more detailed information on each probe here (though you might have to register to view them):
https://www.affymetrix.com/LinkServlet?probeset=<probesetID>
Since different probes may work better or worse against their targets, maybe the limitation was set low on purpose since this kind of data is better suited for looking at a specific target in multiple tissues/cells/conditions rather than multiple gene targets in single tissues. Not saying it can't be done, but it might be a bit trickier than it sounds.

[sindrle]

Ok, thank you. Unfortunatly I have little experience with Micro Array, but I guess Ill manage.