Gene set similarity searches in public databases
Posted 15 May 2011 - 01:11 AM
Posted 15 May 2011 - 08:02 AM
ON what platform was your microarray done and what type of ID (Entrez gene ID, Ensembl ID, gene symbol, etc) did you use as input for the GO analysis, where id you get them? What organism are you working on?
Posted 15 May 2011 - 06:38 PM
Posted 17 May 2011 - 07:49 PM
For GO analysis, if you found 100 genes overexpressed in your cancer samples and you want to know what functional categories those genes represent, you don't need additional datasets as references because you must already have control data such as data from normal tissues and that is how you know the 100 genes are overexpressed. when you apply GO analysis, the software will have these numbers from your data: total number of genes on the array, number of overexpressed and downregulated genes, total number of human genes in GO databases, number of genes in each GO category. If for example there are 10 (0.05%) genes in anti-apoptosis category out of 20k total human genes, and 5 out of 100 (5%) overexpressed genes are from anti-apoptosis category, then your overexpression genes are overrepresented by anti-apoptotic genes. This is what you will get from GO analysis.
Posted 23 May 2011 - 01:56 AM
Sounds like the problem is I didn't do my GO analysis the right way. Do I always have to input the "background" gene list when I do the GO analysis e.g. the whole Illumina HT-12 probe list in my case? I use DAVID but it doesn't make it compulsory to input the background list. Can you pls recommend me some GO programs that you think are good?