One of the challenges with reading so many papers about pancreatic cancer is learning about the pathways and the cellular processes that they support. The NCI‘s Pathway Interaction Database, and Wikipathways are two good resources for learning more about pathways. However, none of these resources provide narratives that describe the details of the process.
Recently, as I was trawling through the list of candidate papers for the Pancreatic Cancer Genomics group, I stumbled across the NCBI’s Biosystems web application. This resource does provide a high-level narrative about the molecules in a pathway.
In addition, Biosystems lets you:
- explore the pathways involved in a particular disease.
- find pathways where a particular gene, protein or small molecule plays a role
- find 3D structures for proteins found in a pathway
- input a gene list, and find a ranked list of pathways in which those genes play a role
- input a gene list, and find a ranked list of pathways in which those genes are under/over expressed
You can also access Biosystems programmatically through NCBI’s eUtilities framework.
On the whole, this looks like a valuable resource for anyone trying to understand the role of a potential drug target in various pathways.