Are there any current efforts to gather C.elegans microarray data sets into a single repository? There are some databases out there (e.g. Publime) that store lists of regulated genes from different experiments, and I was wondering if there was anything like that in the works for C.elegans?
Thanks!
Hi,
WormBase has a collection of C. elegans microarray datasets. There are 34 of them currently available and more are scheduled to be added as they get published. You can get a list of them by running the following query from the WormBase query language page ( http://www.wormbase.org/db/searches/wb_query ):
find paper microarray_experiment
Admittedly, there are no extensive tools that allow one to analyze the data within WormBase itself (one can still explore related data such as experimental conditions used, clustering information, etc.). If you want to analyze data locally, you can download either complete datasets or data for a list of probes using this form:
http://elbrus.caltech.edu/cgi-bin/igor/microarraytools/dump_microarray_data_mysql.cgi
Igor.
P.S. There is also a set of SAGE (Serial Analysis of Gene Expression, which is another technique for assessing gene expression levels on whole-genome scale) libraries available in WormBase that may be of interest to you as well.
Thanks for the information Igor. Is there a way to download the query results as a tab delimited text file? I’ve tried copying the output but the column spacing does not seem to be preserved.
In principle, you should be able to just right-click on the page, save it locally and then import it into Excel or OpenOffice - it is formatted as a tab-delimited file. However, I see that it is not working properly in Firefox. I’ll try to fix that, but in the meantime you can save the file in the correct format using IE (I’m ashamed of suggesting this), Safari or Konqueror if you’re using Windows, OSX or Linux, respectively. You can also select ‘File’ as an output option - results will be directly saved on your computer in the tab-delimited format.
Hope this helps.
Igor.
Yes, Thanks Igor that works!
All microarray data can also be downloaded as one file from this ftp site: