I am PhD.candidate and a user of the program Pathviews. I have run the API in Bash shell mainly, but I do control this to the web based version outcome. I do several automated analyses of DE-list from bovine embryos. In some of these analyses, the list contains 6 differentially expressed genes, and in other over 1500. I do however always get a result of 3 pathways as an outcome, which I find unlikely. Is this a standard setting, and how do I get around this? Of course, I am looking for pathways of all my DE genes. The API I use is generated from the webpage.
Let me also inform you, that I am not a very competent programmer, but a humble veterinarian using Pathviews for the first time.