Tag Archives: Pathway Analysis


Friday SNPpets

This week’s SNPpets include bringing pharmacogenomics to the clinic, de novo assembly with long reads, a good example of using BioGPS, iDNA (it’s not what you think), places for women in science, law enforcement poking around consumer genomics sites, analysis of consumer sites, a neuroscience vs genetics smackdown begins, a new pathway tool, and a new citation metric. And more….

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

http://questiongene.com/baming-with-bacteriophage/ [need tweet here]

New Reactome Release Announced Today

Mary got an announcement about a new Reactome release today through the Gofriends mailing list. You can read the announcement, and I’ll share my brief analysis of the release here. I’ve been playing with the new functions this afternoon.

If you check out the release, or examine the image I’ve included, you’ll notice immediately that the homepage has been changed significantly. The homepage previously displayed a huge interactive map and a listing of superpathways under that, with navigation options along the top. The homepage is now much more an information source rather than an immediate entry into the pathways. The top navigation tabs are still available with much the same tools, except the SkyPainter tool is no longer listed. The main panel of the page now contains an ‘About’ area, an image of ‘the pathway of the month’ (which can be clicked for immediate access to the pathway display), and a News and Notes area. On the left is a new navigation area with a keyword search window, buttons to tools (Pathway browser, Pathway Analysis, Species Comparison and Expression Analysis), then multiple download options, a ‘try this’ area that takes you to the Pathway Analysis tool interface, and an area to add your comments about the new release.

The new Pathway Browser interface opens with a left panel listing pathways, and the right panel empty. A user clicks on any desired pathway & then selects the subpathway that they want to be displayed in the main panel. The main panel displays a zoomed in area of the pathway. Additionally a tiny panel opens between the list and the pathway panel with an overview image of the full pathway. This can be used to navigate to the desired area of the pathway in the larger, zoomed-in panel. There are also a variety of analysis, annotation and uploading functions available from a tab in the left panel, and a details report can be opened as a lower (4th) panel by clicking a small arrow head.

The Pathway Analysis tool appears to have replaced the SkyPainter tool. Like the SkyPainter it takes a list of IDs & analyzes them for associated pathways. While the SkyPainter tool color-coded pathway diagrams with over represented pathways and listed statistically over represented pathways, the analysis tool provides a list of all associated pathways for each gene or protein in the users ID list. From the report users can link to the Pathway Browser displays to further explore the individual pathways.

The Compare Species and Expression Analysis tools allow users to either compare pathways across two species, or to map expression data onto pathway images. Both have example datasets that you can click & run. Other powerful tools, such as the advanced search, BioMart search function, PathFinder and Small Molecule Search all appear to be available and largely unchanged, which is cool.

We’ll of course be updating our full Reactome tutorial to reflect the changes in detail – after we give the release a bit of time to be sure everything is stable. :)