Learning More About Pathways

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Logo of the United States National Center for Biotechnology Information, a part of the National Library of Medicine, itself part of the National Institutes of Health. Français : Logo du NCBI (Photo credit: Wikipedia)

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.


About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
This entry was posted in Informatics, pancreatic cancer and tagged , , , , . Bookmark the permalink.

2 Responses to Learning More About Pathways

  1. Sandeep Basu says:

    how to find a pathway for a particular gene?

    • aspenbio says:

      Did you try the “Quick Start Guides” link shown on the front page of the BioSystems website? It has tutorials that show how to use BioSystems.

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