I was interested in analyzing and constructing a signaling pathways when comparing two different states (such as control vs disease) of a micro-array gene expression database. Which software tools would be recommendable for this?
We have an application designed specifically for this called iPathwayGuide (www.iPathwayGuide.com). This is a web-based application that doesn't require any coding experience. Simply upload your CEL files in the groups your wish to analyze. iPathwayGuide will QC check and normalize (GCRMA) the CEL files automatically. Information about DEGs, Predicted miRNAs, GO terms, Pathways and diseases is provided in minutes. If you have multiple analyses, you can generate a meta report that will give you information about the overlap between the datasets. Here's are a brief video.