The basics are always the same regarding of the assay. The first step is to map the results of your assays onto genes. The assay can be very different but in most cases you can map the results on genes. For instance, for a methylation assay, you could associate each differentially methylated region to the gene immediately downstream of it. There will be some that won’t be mapped, but most areas that have an effect on transcriptional control are expected to be mapped correctly. Then you calculate an effect size. that can be a log fold change of differential expression or differential protein abundance or methylation, etc. It is often possible to calculate a p-value, as well. Once you have genes, effect sizes, and p-values, you can upload this in iPathwayGuide. You should specify the type of assay the data came from so you can do a meta-analysis later integrating multiple types of data, if those additional data become available.
