iPathwayGuide FAQs

The report is deprecated" message is there to inform you that the report is not based on the latest knowledge available. If you choose to update the report, the analysis is done again, from scratch, with the latest version of [...]

Prepare a list of genes with a header "Symbol", in one single column. Please use HGNC/MGI symbols only. You can use in-built reference background gene set, or a custom background gene set for enrichment analysis If you opt for enrichment [...]

Of course, you are allowed to publish any and all figures from our software. That’s the whole point. The software is meant to create figures and give you results that can be directly published so you can save time and [...]

Regarding the figures, you need to download them in .SVG format from iPathwayGuide. Any downloadable figure in our software can be downloaded as SVG. The SVG is a scalable vector format that can scale to any size and offers perfect [...]

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. [...]

iPathwayGuide supports directly human, mouse and rat. For other organisms, you need to first map your genes to orthologs. Many of our users have done this very successfully. Here is an example in which iPathwayGuide was used to make important [...]

The answer here is very similar to the one above. When you change the organism, the annotations will be different. This would be a totally different experiment basically. This is an additional reason for which this has to be a [...]

When you change the p-value, the number of differentially expressed genes will change. That in turn, will change every single results in every single type of analysis performed: GO terms, pathway, upstream regulator, drugs, mechanisms, etc. The results will be [...]

On the Pathways tab, on the right hand side, “pathway details” then “Gene table” then the “+" sign. When you click on that, you will see a table with the genes on the pathway. there you can sort, search for [...]

On your dashboard, you can click on the little shopping cart and then click on “purchase with balance.” The report will become available right away.

When one shares a report with somebody else, the recipient gets a link and they will be able to access the report and do everything that the owner can do. The owner has the opportunity to decide whether the recipient [...]

Yes. Please download it here. Open (PDF)

iPathwayGuide supports analysis of Human, mouse, and rat. It supports the following files formats: CuffDiff DESeq ​EdgeR SAS/JMP Genomics nSolver (NanoString Technologies) Generic tab delimited .txt file (must contain gene symbol or uniprot ID, log2FC, p-value) SCIEX SWATH 2.0 [...]

Please make sure your are using the "...gene_exp.diff" file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has [...]