nodalpoint.org - Gene expression analysis - Comments

more on pathways

vndinu — Sat, 16 Jun 2007 17:45:22 -0400

Interesting comments, some of the commercial pathway analysis tools are indeed quite good. I'm also working on a pathway-based analysis of genotype data, the paper is in press in the Journal of Biomedical Informatics and the tool will be made publicly available soon. valentin dinu, http://www.dinuinformatics.info

Pathway analysys and discovery

thex-raykid — Sun, 21 Jan 2007 18:04:34 -0500

It's an old discussion but it still comes out on google search...
I was recently trying to find good pathway analysis software (preferably free), reviews or anything. What I found interesting is DAVID, which is not really pathway analysis soft but quite useful tool anyway, and Pathway Discovery site with some great tips. Hope this helps.

Commercial posts

dbodde — Mon, 05 Jun 2006 10:50:32 -0400

Yes, I am. That policy sounds fair enough..

Doug Bodde

So I assume you're Douglas

Greg — Mon, 05 Jun 2006 09:07:33 -0400

So I assume you're Douglas Bodde, VP Sales and Marketing from Biomind ?

I'm am not fundamentally against biotech companies posting informative news/announcements on nodalpoint. However cutting and pasting from press releases and white papers is the wrong way of going about it. It comes across as a little bit contemptuous of the people who run/frequent the site.

Please contact me if you have any questions reading site policy wrt companies/advertising etc. or reply to the post. If I don't hear anything shortly I'll unpublish this post.

Ironically this has already been indexed by google, I came across it today doing a search for 'supervised leaning and biomarkers'. I didn't see biomind.com there...

I think this should be

Greg — Thu, 02 Mar 2006 04:24:40 -0500

I think this should be re-posted in the Announcements forum.

this post sponsored by...

Neil — Wed, 05 Oct 2005 20:05:16 -0400

...it's easy to spot posts from people promoting companies, you know :)

Our original poster specified an open source solution - I think he wants it to work for longer than 30 days.

Ingenuity Pathways Analysis

PathwaysGuy — Wed, 05 Oct 2005 18:46:32 -0400

Have you tried the new ingenuity Pathways Analysis 3.0 ? You can get a new free trial. I am ready to bet that this one is going to make it big time.

Belief

Neil — Thu, 22 Sep 2005 20:43:48 -0400

Who cares what I believe? They're all the rage, so they must be good :)

Since you asked though - my personal feeling is that microarrays are a great idea in principle but are rather let down by a lot of the practice. If your northern or southern blot is afflicted by high background or poor visualisation, you spend some time optimising the hybridisation conditions. Conversely, when people have the same problems with microarrays (which to me are just northern blots on steroids), they instantly leap to a wide assortment of complex statistical methods to massage their data. I'd have more faith in microarray results if as much time was put into improving experimental technique and design as goes into normalisation.

The Australian academic community is also plagued by people who confuse hype with substance and tend to latch onto techniques, then equate them with the whole field - "microarrays = bioinformatics", "proteomics = bioinformatics" and so on. I think it's because they can't conceive of what standalone computational analysis entails and need to tie it to what they understand, i.e. molecular biology.

Why the shock?

Anonymous — Thu, 22 Sep 2005 17:01:50 -0400

Just curious. Is it your belief that microarrays generally aren't useful?

Check out cytoscape

Anonymous — Tue, 08 Feb 2005 22:29:44 -0500

Cytoscape (www.cytoscape.org) is an open source network analysis workbench. The raw program doesn't know anything about biological analyses, but you can download and install all kinds of cool plug-ins (see website) that do specific tasks.

I can recommend

mseewald — Sat, 01 Jan 2005 12:23:00 -0500

I can recommend Pathway Assist. IMHO this is a cutting-edge product and shows where things can/should go in the future. There are many things to improve, performance for example. Nevertheless, the program opens you a whole new look at literature and networks/pathways. The data is derived from PubMed by literature mining. Quality of the networks is surprisingly good.

Open-source software, on the other hand, is lagging behind. Projects like Biocarta, GenMAPP etc. are really great. However they only provide static snapshots of pathways ("cartoons"). You can not interactively work with the software to explore the pathways behind.

accelerating pathway analysis

Anonymous — Thu, 09 Dec 2004 12:32:04 -0500

You may want to take a look at the product below, if you are using open source analytics tools, TB will help you build a worflow and execute them in an distributed environment...company is called turboworx

i hope this helps

TurboWorx Builder

rule based approach

shawnh — Tue, 07 Dec 2004 01:09:55 -0500

http://www.genepath.org/

Open-source pathway analysis

WhiskerBiscuit — Fri, 26 Nov 2004 16:47:17 -0500

It sort of depends on what exactly you want the software to do, but there's a free package called GenMAPP that allows one to map the results of array experiments onto known pathways. There are lots of pre-existing templates for known pathways and the opportunity to enter your own if you like:

http://www.genmapp.org

Hope that helps.

> Good afternoon,
>
> I wonder if anyone has had positive experiences with any open-source pathway
> analysis programs? I am looking for something more than Netaffx for my
> Affymetrix data. The free trial of Ingenuity Systems' pathway analysis
> software founded on a hand-curated database has been very impressive, but the
> software is really expensive.

Application for Milano

ranrub — Tue, 16 Nov 2004 05:50:21 -0500

Let me give you an example. When performing a microarray experiment in which you test expression response to p53 (a DNA damage-related transcription factor and Very Important Protein), you get a list of 150 genes that were significantly up- or down-regulated. Now you want to find information about these genes. Milano enables you to perform automatic searches in the literature for these genes and cross them with experiment-specific search terms.
For example, searching these genes with the term 'p53', will give you positive hits on genes that co-appeared in articles with their putative regulator (as detected in the microarray experiment). This enables you to find known p53 targets, or even regulatory feed-back loops - if you find regulators of p53. Other intersting applications can be thought of.