Protocol Online logo
Top : New Forum Archives (2009-): : Macroarray and Microarray

Pathway Analysis of Microarray data - (Jan/22/2012 )

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.




There are a few free pathway editing or drawing tools available.

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).

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.

Biocarta does provide pathway templates for you to use with Freehand or illustrator.

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.


Thanx PCRMAN.....that was very helpful. will try these out today.