Tag Archives: networks

Friday SNPpets

This week’s SNPpets include mining disease genes with PPI and co-regulation networks, DNA and the law, great posts on germline genetic engineering moratorium discussions, a bioinformatics “middle class”, new human genome assembly models, and more….


Welcome 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…

What’s the Answers? (build gene networks from literature)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity 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.

Recently someone came by to ask about ways to extract useful information from the literature and construct a network from that. Respondents offered helpful software–but also nice guidance on thinking about how the networks need to be thought about in an organism:

Question: Building gene regulatory networks from literature

Hi everyone!!

Does anyone know of any available software that would build gene regulatory networks from literature alone?

Thanks!

Diana

The first answer offered some software to consider, but the second answer (at least as currently ordered) provided thoughtful commentary on aspects of this to consider beyond the literature.  I thought that was a nice balance. Check out the discussion.

What’s the Answer? Open Thread (gene networks)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity 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:

I have 10 genes linked to a particular disease (for the sake of example say cancer).
I want to build a gene network for these 10 genes.
Any web based tools available which can do the job?

I immediately thought of GeneMania (publicly available OpenHelix tutorial) and STRING (tutorial, by subscription) . The best answer beat me too it, with a lot of other excellent tools. Go check it out.

 

 

 

 

Tip of the Week: GeneMANIA for Fast Gene Function Predictions

I am happily the lucky scientist here at OpenHelix who has been selected to create a full tutorial on a network resource named GeneMANIA, but I just couldn’t wait to share some of the details about this resource’s great features. GeneMANIA stands for Multiple Association Network Integration Algorithm. Users can either input a single gene and see interaction networks associated with the gene, or (more powerfully) to enter a list of related genes and use GeneMANIA’s ‘state-of-the-art analysis algorithm’ to quickly and easily find additional related genes.

GeneMANIA allows a  scientist with no prior training in computational bioinformatics to easily use their gene list of interest to search a customized list of published functional genomics publications, as well as a wide variety of public databases, and receive the results of their analysis in an easy to interpret PDF report. Users can even upload their own important datasets and affect how the algorithm scores each gene and dataset. I  cannot cover all this functionality in this short tip – you’ll have to see our tutorial for that – but here I will show you how to do a basic search and some of the display features of GeneMANIA.

GeneMANIA stands for Multiple Association Network Integration Algorithm. For more information about it, please see this 2008 GeneMANIA publication, or the GeneMANIA documentation.

Reactome new release, now with axon guidance!

Last night I had coffee with good friends in Davis Square and I mentioned that we had this blog.  One of the friends (a linguistics scholar) seemed excited by the prospect until I told her the topic.  She’s not nearly as excited by new software and scientific data as I am :)

It cracked me up this morning when I read the Reactome news letter–my first thought was: cool, axon guidance pathways!  And I imagined my friend’s bemused look….

Anyway, there’s a new Reactome release.  Here’s some of the new stuff content-wise:

New content. As part of a project to annotate the general process of cell motility and its involvement in key biological processes, Version 29 introduces a new topic, Axon guidance, with material now available for NCAM signaling in neurite outgrowth. Pathway topics updated with new curated events in this release include: Synaptic transmission (Glutamate Binding, Activation of AMPA Receptors, and Synaptic Plasticity), DNA Repair (regulation of FANCD2 and FANCI activity in the Fanconi Anemia pathway), and pathways whose dysfunction plays a major role in the development of diabetes (Regulation of insulin secretion and Unfolded protein response). With the annotation of G-coupled protein receptors (GPCRs) for eicosanoids, leukotrienes, nucleotide-like (purinergic) molecules, LPA and lysosphingolipids, opsins, secretins, and GABA and related molecules (class C/3 receptors), our annotation of interactions between GPCRs and their ligands is essentially complete. The Telomere Maintenance pathway has been revised in this release. Updated release statistics are available.

If you are interested in keeping up with Reactome their mailing list is here: http://mail.reactome.org/mailman/listinfo/reactome-announce

Software bonanza…

Still enjoying the ICSB meeting, and it is a gorgeous fallish morning in Göteborg. What a great city and terrific people here. Not entirely sure I want to come home….

My brain is approaching “full” already, and there are still several days to go. I’ll have a lot of tools to talk about in the coming weeks as I check more of them out. But I wanted to talk about a couple of neat tools that I have heard about so far. First–CellDesigner 4.0, that I mentioned the other day, was a good choice of tutorials to attend for sure. You can access their tutorial material here. Turns out they are also about to release a web-based version of this that will be a collaborative community editing tool for networks and pathways. It is called Payao–which I’m told means a type of “fish-aggregating device” according to their poster. I was unable to catch the poster authors so far to discuss it further, but it looked like a neat tool. I can’t find a release on the web yet and there was no URL on the poster. I’ll try to track them down again today.

Update: Found it here http://celldesigner.org/payao/payaopreview.html

Another fun tool (which I haven’t had a chance to use much yet) is BioMyn. The idea behind BioMyn is that it is something like a Google search for systems biology and other relevant biological data types. It aggregates a lot tools into a single search, here’s a partial list: ensembl, MINT, GAD, HPRD, Corum, InterPro, PDB, OMIM, GO, Reactome, KEGG, UniProt, HiMap, IntAct, GNF, and DIP. I spoke to Fidel Ramirez, the creator, about this tool and he was very eager to have users and feedback on this new beta phase. He was saying that people have suggested the results link should be re-organized a bit. If you do a search you get a list of results and some context. The link at the top goes to your “best” resource hit–leaving BioMyn. But if you click the link at the bottom of the result ( View all annotations for ) you go to the aggregated results in BioMyn. Organized into a collection of data in tabs, you can find a wealth of information on this gene. You can find gene links, of course, but also diseases, pathways, interactions, GO terms, and on and on. Anyway–check it out. And keep in mind it is beta. Feel free to offer feedback here and I will pass it along to the developers–they don’t have a feedback link on the site yet. But they do have a blog, I suppose you could put comments over there. In fact, I’ll suggest that to the team today if I see them.