This week’s Video Tip of the Week demonstrates PANDA, a tool for generating and examining annotations that are available for a list of genes, and evaluating them in the context of pathways. Two great tastes that taste great together, you know? So have a look at how PANDA can help you and your team to annotate lists with both curated and personalized details, and see relevant connections among items in your lists. Note: all the data appears to be human–there are no actual pandas here, except one of the available icons to use to designate your gene list. If you are looking for actual panda genome stuff, try here.
I began by looking into the paper recently out in PeerJ, linked below. It sets out their goal of helping you to link all the -omics types of information you may be generating or collecting. Here’s a quick description of their tool from their abstract:
We have developed PANDA (Pathway AND Annotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB.
Their nice intro video here will introduce the basic features. One thing though–the sample list that is used has been moved to the GitHub repository, and the one used is GENELISTB in the EXAMPLES folder. I copied that to an excel file and did the same thing as illustrated in the video and it worked great. [And yes, I know y'all hate excel, but it works for biologists, they'll get the annotation thing this way.]
It was really easy to move from my sample gene list into a KEGG pathway, and so clear which genes in my list were components of this pathway because of the overlay icon that PANDA let you assign to your data. And you can further overlay that with the DGIdb, OMIM, HPO (yes, I mentioned to you recently we were going to need to understand this), MalaCards, and PharmGKB links too.
So the idea is whatever kind of -omics data you have, as long as it is tied to a gene, you can upload it and explore the relationships in more detail with these handy mappings and additional details.
And there is a way for you to have multiple colleagues access your annotation set and add further details.
But you aren’t limited to the pathways already in the PANDA system, there are also ways to customize what you know about your pathways and annotations. There is a second video that will offer more detail on that using a network with Cytoscape. You can get the other video from the Mayo Bioinformatics YouTube channel or on their site.
Hart, S., Moore, R., Zimmermann, M., Oliver, G., Egan, J., Bryce, A., & Kocher, J. (2015). PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data PeerJ, 3 DOI: 10.7717/peerj.970