Question: Is There A Tool To Give A Visual Output Of A Pathway And Expression Data?
6
gravatar for Timtico
8.8 years ago by
Timtico330
NL
Timtico330 wrote:

I'm looking for a tool that lets me combine expression data with a pathway map (like glycolysis in Kegg) in a visual way. e.g. by giving numeric or color annotations to certain parts of the pathway

Preferably the tool should be simple to use (as it is meant for one of my students), but also tools which require a bit more programming (Bioconductor libraries) are welcomed.

ADD COMMENTlink modified 6.5 years ago by B. Arman Aksoy1.2k • written 8.8 years ago by Timtico330
4
gravatar for Pablo Pareja
8.8 years ago by
Pablo Pareja1.6k
Granada, Spain
Pablo Pareja1.6k wrote:

What about Gephi ?

I used it together with Bio4j for some gene-ontology visualizations and must say I'm quite happy so far. Here you have a couple of links with some samples:

http://blog.bio4j.com/2011/04/go-annotation-graph-visualizations-with-bio4j-go-tools-gephi-toolkit-sigma-project/

http://blog.ohnosequences.com/2011/03/playing-with-gephi-bio4j-and-go/

ADD COMMENTlink modified 8 months ago by RamRS27k • written 8.8 years ago by Pablo Pareja1.6k
3
gravatar for Russh
8.8 years ago by
Russh1.2k
U. Liverpool
Russh1.2k wrote:

or try Cytoscape

ADD COMMENTlink written 8.8 years ago by Russh1.2k
2

Might help to indicate what plugin he should use.

ADD REPLYlink written 8.8 years ago by Qdjm1.9k

doesn't need plugins

ADD REPLYlink written 8.8 years ago by Russh1.2k

Or RCytoscape to drive Cytoscape from within R.

ADD REPLYlink written 8.8 years ago by Martin Morgan1.6k
2
gravatar for Qdjm
8.8 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

Try GenMaPP.

ADD COMMENTlink written 8.8 years ago by Qdjm1.9k
1
gravatar for Neilfws
8.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You may like to try FunNet. There's a web server version and also an R package.

It takes a little effort to figure out how it works but basically, it does what you describe: takes expression data and maps it onto KEGG (as well as GO). See the tutorial for details.

The output can also be loaded into Cytoscape for visualization.

ADD COMMENTlink written 8.8 years ago by Neilfws48k
1
gravatar for Philippe
8.8 years ago by
Philippe1.9k
Barcelona, Spain.
Philippe1.9k wrote:

I didn't try the programs mentioned above so I don't know if they are more convenient than the solutions I'll suggest:

  1. Ipath. It is only a web interface to display KEGG maps but the maps are customizable. I could not try it before and it is currently not working on my computer but their help page teaches how to customize the maps. The only drawback and that you need to first create a mapping file (Kegg Id to color) and then load it into Ipath. I agree this can be tedious if you want to do this several times.
  2. R and KeggML (KGML, an XML format) files. With the KEGGgraph and KEGG.db libraries (part of Bioconductor) you can easily parse a KGML file (function parseKGML2Graph). This will return an object containing the nodes, edges,... You can draw this graphs and modify them, specifying colors for edges or nodes or changing the shape of the nodes for example. You can then simply specify the colours based on the gene expression level. I did this few months ago and it works quite well, one drawback is that it becomes a bit hard to read if there is many nodes/edges. This requires a bit of coding but it is quite well documented and might not need a lot of time if you are used to R.
ADD COMMENTlink written 8.8 years ago by Philippe1.9k
1
gravatar for Bert Overduin
8.8 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

Or try the Expression Analysis module of Reactome. To get an idea what is possible, have a look at the documentation.

ADD COMMENTlink written 8.8 years ago by Bert Overduin3.7k
0
gravatar for B. Arman Aksoy
6.5 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

You can also try ChiBE. It can load pathways from Pathway Commons and visualize it in an SBGN-like way. It also lets you overlay expression data on top of the nodes from a local file, from GEO or cBioPortal.

Here is the URL to the project page: http://code.google.com/p/chibe/

ADD COMMENTlink written 6.5 years ago by B. Arman Aksoy1.2k
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