Dear All...
I have some gene expression data from cDNA microarrays. Now, I want to find out which pathways are significantly different between my groups. Using DAVID online analysis tool, I uploaded a gene list having all differentially expressed genes (up and down regulated) and got hold of all dysregulated pathways. However, I wish to colour the differentially expressed genes in the pathway, like, red for down and green for upregulated pathways.
Can somebody please instruct me how to obtain such a pathway diagram? Using any software or online tool. Only limitation is that I need something which is freely accessible...can't purchase any softwares.
Thanx!
Maverick
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2 replies to this topic
#2
pcrman
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Posted 22 January 2012 - 10:06 AM
There are a few free pathway editing or drawing tools available.
http://kgml-ed.ipk-g...stallation.html
KGML-ED allows the dynamic exploration and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Pathway files are loaded and transformed into a graph network which may be modified to fulfill user-specific needs (e.g. it is possible, to delete or add network elements, change labels and colors).
http://www.genmapp.o...wnload_v2.1.php
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web.
BioCart:
Biocarta does provide pathway templates for you to use with Freehand or illustrator.
http://www.biocarta....genes/index.asp
Download Pathway Tools
Below are links that will allow you to download the Biocarta templates which you can use in the creation of your own Pathways.
http://kgml-ed.ipk-g...stallation.html
KGML-ED allows the dynamic exploration and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Pathway files are loaded and transformed into a graph network which may be modified to fulfill user-specific needs (e.g. it is possible, to delete or add network elements, change labels and colors).
http://www.genmapp.o...wnload_v2.1.php
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web.
BioCart:
Biocarta does provide pathway templates for you to use with Freehand or illustrator.
http://www.biocarta....genes/index.asp
Download Pathway Tools
Below are links that will allow you to download the Biocarta templates which you can use in the creation of your own Pathways.
#3
maverick3006
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Posted 22 January 2012 - 03:33 PM
Thanx PCRMAN.....that was very helpful. will try these out today.
