What’s the Answer? thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:

Tools for visualizing significantly altered pathways and related genes in a pathway graph ?

Some pathways were significantly altered on my microarray data. I want to highlight these pathways and the related genes on a single pathway graph. I tried iPath and found there were some conflicts of edges when I tried to color up- and down-regulated genes in different colors. Therefore, I want to know if there are some other tools for highlighting pathways and genes simultaneously.                      –by Balance

Answer:

Although no single answers was selected in the ensuing discussion, there was a good discussion of various tools that might solve this problem. And there was also reference to a related question that provided more tools for pathway analysis of microarray data. You can find that question at the top of the “Related” question list on the right side of the page.