Tag Archives: pathway

new_reactome

Video Tip of the Week: New Reactome Pathway Portal 3.0

new_reactomeThe Reactome pathway browser has long been a favorite of ours. We’ve watched it evolve over the years, and continue to appreciate the organization and features that it provides for exploring pathways and interactions across a range of species.

From the mailing list recently, I learned about a new version of the Reactome Pathway Portal, v3.0, that’s now available for everyone. I’ll post a piece of it here, but you can click through to their announcement for full details.

The Reactome team announces the release of our new pathway browser, accessible through our web site http://www.reactome.org/PathwayBrowser/ . The browser provides faster and more reliable navigation of our content and better access to our analysis tools. Improvements include improved and customizable color schemes, and the ability to search for terms within an individual pathway diagram using names, gene names and identifiers including identifiers for molecules hidden within complexes and molecule sets displayed in the diagram. The browser “back” and “forward” buttons allow the user to review every selection made to reach the current view. The level of detail shown in diagrams is zoom-dependent, so recurring small molecules like ATP and water fade out and colored overlays appear to identify subpathways appear as the user zooms out, providing a more legible and informative overview.

So their great foundation remains, but navigation is improved and other features have changed in this update. Delightfully, they have created a short intro video as well, and that becomes our Video Tip of the Week today. Note: there’s no audio with this, watch for the annotations.

I expect that there will be a paper to come with the new details, but I wasn’t able to locate it just yet. I’ll add back the reference when I find it (and yes, I do trawl the Advance Access section of NAR to see what’s coming in the next database issue pretty regularly….).

Quick links:

Reactome main site: http://www.reactome.org

Reactome new pathway browser: http://www.reactome.org/PathwayBrowser

Reference:
Croft, D., Mundo, A., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., & D’Eustachio, P. (2013). The Reactome pathway knowledgebase Nucleic Acids Research, 42 (D1) DOI: 10.1093/nar/gkt1102

PathWhiz sample

Video Tip of the Week: PathWhiz for graphical appeal and computational readability

“Pathway diagrams are the road maps of biology.” This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announced. The NAR database issue in January and the mid-year web server issue are perfectly timed items that I can content mine all year ’round. And I am always drawn to the tools which are offering better visualizations for data. PathWhiz is offering better road maps. So I definitely wanted to take a look.

They note that historically pathway data has been artistically rendered for print applications like papers and posters, and can be quite engaging and attractive. But actually working with pathways in computational settings can be a bit more, um, sterile–I guess I would characterize it. Their goal seems to be to merge the two: better options for graphical components, but still machine-readable for further manipulation and exploration. They summarize their goal in this hybrid approach:

PathWhiz is essentially a web server designed for the facile creation of colourful, visually pleasing and biologically accurate pathway diagrams that are machine-readable, interactive and fully web compatible.

The paper goes on to describe a lot of the foundational concepts and the implementation. There are important technical aspects covered about the formats and file types. But the best way to get a feeling for it is their intro video. You can also access that on their tutorial page and I’ll include it here.

Mid-way through this PathWhiz video 1, they show you the difference between a KEGG, Reactome, and WikiPathways visualization to give you a sense of the differences. (~4:15). A part II video is coming, but not available yet. It has posted since I started this.

Look through the “legends” area to see the kind of handy diagrams you might need–molecules, membranes, or cellular organelles, or even tissues like brain or liver. Tab through the different types of graphics that are available to get a sense of how your pathways could look rendered in the PathWhiz system. PathWhiz sampleYou can try it out easily too: there’s a “guest” mode where you can just kick the tires. Or you can create a login and work on some of the ones that might be useful for your work and your presentations and papers. Those can be saved and locked, but can also be cloned and expanded on by other people. You can also get a sense of what some of the more mature diagrams can look like by browsing the pathway collection. I thought this one: 17-alpha-hydroxylase deficiency (CYP17), had nice examples of the tissue (kidney) and organelles involved that quickly give you a grasp of what’s going on and where. I’ve just shown a small part of it in this image, it’s much more detailed at full size. You can zoom in to see the pathway components. And you can see from here that the details are exportable in a number of ways by clicking the “Downloads” tab.

So for better representations for humans to view, while also preserving the important functions that computational renderings can offer, PathWhiz is worth a look. Go over and try it out.

Quick links:

PathWhiz: http://smpdb.ca/pathwhiz

PathWhiz legends to see the graphics: http://smpdb.ca/pathwhiz/legend

Reference:
Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015). Pathways with PathWhiz Nucleic Acids Research, 43 (W1) DOI: 10.1093/nar/gkv399

Benson G (2015). Editorial: annual Web Server Issue in 2015 Nucleic Acids Research, 43 (W1) DOI: 10.1093/nar/gkv581

Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks

This week’s video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week’s tool is the final piece that you need to know about if you want to create the kind of interaction/network diagrams used in the modeling of a system that I covered last week.

The yEd Graph Editor is different than some of the tools. As a corporate product, it doesn’t have

yFiles layouts options in Cytoscape

yFiles layouts options in Cytoscape

the kind of scientific paper trail that some academic tools will. But if you search Google Scholar for “yED Graph Editor” you’ll see people from a wide range of disciplines have used it for their research projects. I first learned about yEd when I was using Cytoscape, and saw that some of the choices for layouts were based on the yEd features. This short overview video from the yWorks folks will explain what some of those layout styles are.

As you can see in this video, the use of yEd is not only for biological interactions–it can do a whole lot of graphing that is entirely unrelated to biology. But the features work for biological networks, and you can customize the graphics to represent your own topic of interest.

There are longer videos with more detail on the use cases for yEd. This one uses a sample flow chart to illustrate the basic editing features. It quickly covers many helpful aspects of establishing and editing a visualization.

You can also find videos from folks who use yEd for their projects on YouTube, some of which might be more specific for a given field of research. But these should give you the basics of why yEd can be used for the types of projects that you saw in the previous tips with Virtually Immune and BioLayoutExpress3D. And like I noted with Virtually Immune, you can get your hands on the files in the Pathway Models collection, and launch a yEd file to go into the features with a detailed example. The complexity you can generate with these models is astonishing.

There was no reference specifically for yEd that I was able to locate, but you can find that lots of people use yEd graph editor on a wide range of research topics in Google Scholar. So if you are looking to see if someone in your research area has used yEd, you may find some examples. If you are going to consider exploring the BioLayout and Virtually Immune tools, it will help to understand the framework. And also as I mentioned in Cytoscape–understanding yEd helped me to grasp the layout options there too. So try out yEd for pathway and network visualization if you have needs for those types of representations in your research and presentations. It’s free to download and use.

Quick links:

yED Graph Editor: http://www.yworks.com/yed

yEd Graph Editor Manual: http://yed.yworks.com/support/manual/index.html

References:

Wright D.W., Tim Angus, Anton J. Enright & Tom C. Freeman (2014). Visualisation of BioPAX Networks using BioLayout Express3D, F1000Research, DOI: http://dx.doi.org/10.12688/f1000research.5499.1

Smoot M.E., K. Ono, J. Ruscheinski, P.-L. Wang & T. Ideker (2010). Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, 27 (3) 431-432. DOI: http://dx.doi.org/10.1093/bioinformatics/btq675

What’s the answer? Genes–>Pathway

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.

Question of the week:

Mapping genes to pathway

Hi!

I have a set of gene identifiers(RefSeq) and I want to know the pathways in which these genes are present along with some statistical score.

Any suggestions for tools.

Thank you

–SNPminer

This is a question we see pretty frequently, and there are a number of tools that can help. The selected answer includes both tool suggestions and some useful references. But other answers also flesh out the options. Have a look at the answers, and add others if you have favorites methods for doing this.

Update–I’ll just note that one of the answers comes from Chris Evelo, and I just saw this tweet about him:

RT @larry_parnell: Nice! Congratulations! @Chris_Evelo just received an Agilent Thought Leader Award to Bridge Pathways, Metabolic Models and Gene Annotations

Congrats to Chris! Check out what a “thought leader” has to say on this topic over at BioStar.

Tip of the Week: PSI Structural Genomics Knowledgebase

Last January I did a tip that featured the monthly Structural Genomics Update, which is essentially a newsletter and article collection from PSI Structural Genomics Knowledgebase (SGKB). However, the update is just one aspect of what SGKB offers. In today’s tip I want to feature the wonderfully efficient ways that Structural Genomics Knowledgebase provides you with to learn about the proteins that you are interested in. What I tried to stress in this tip is the different emphasis that Structural Genomics has compared to the RCSB PDB. The RCSB PDB is a GREAT resource, which we also have free tutorial on, but it was created by and for structural biologists. Its displays feature angstroms, angles, conformers and more.

Me, I’m a Molecular Biologist by training & I think about proteins in terms of genomes, pathways, medical relevance, molecular functions, and the like. The SGKB thinks like me, and even organizes information and links into those sorts of categories. I really like how it presents protein information to me, and in the process how it eases me into thinking about the more ‘hard core’ structural details that I see in PDB. The tip is just a teaser taste of the SGKB – if I peak your interest, please do check out OpenHelix’s full, free introductory tutorial on the PSI-SGKB (sponsored by PSI SGKB) as well as the site itself. You never know, you might just learn to love a crystal! :^)

Tip of the Week: Molecular INTeraction Database (MINT)

mint_thumbnail.jpgMINT, the Molecular INTeraction Database, is so much fun to use. I know–there is high-quality curated information from the scientific literature. And that’s the real point. But quite frankly, I just love to examine the protein-protein interactions in the MINT viewer. In this brief (about 3 minutes) exploration of some of the high-level features of MINT I will offer a taste of how fun and informative this resource is.
mentuccia_small.gif
A team at the University of Rome brings MINT to you. Check it out here: http://mint.bio.uniroma2.it/mint/

But at just a few minutes, we can’t provide the full detail about how to understand the graphics and how to use the site most effectively. We have a full tutorial on MINT that you might want to examine if this is a tool you would want to use on a regular basis.

And for more detail on the background and goals of MINT you should check out their paper. From their abstract:

Over the past few years the number of curated physical interactions has soared to over 95000.

That’s a lot of MINT. If you are like me and the previous owners of your house planted mint, you’ll understand the scope :)

Microsoft Surface, not quite science – yet…

OK, this is a quick post, but I just had to share this video that I saw last night. It is about a ‘surface computer’ being developed by Microsoft. It may not be bioinformatics yet, but I predict it will be shortly after it gets to market – I mean, can you imagine examining KEGG or Reactome pathways with this? Thinking about it makes my mouth water, scientifically speaking!