How to map genes to pathways and show results graphiclly?

[czc]

Hi guys,

I've done RNA-seq analysis of differentiated expression genes (DEGs). I'd like to map those genes onto pathways I'm interested. I know DAVID can simply generate an enrichment result by merely providing gene list. However, it cannot show the DEGs in the pathways as a graph. KEGG database also has interface to highlight genes in the pathways. But I'm confused by the gene IDs as well as KEGG ids.

In sum, my question is given a list of pathways and a set of genes, does anyone have some suggestion on how to highlight those genes (upregulated and downregulated with different colors) in the pathways I'm interested?

Thank you very much in advance!

[turnersd]

I like the Bioconductor SPIA package.

[dawe]

In sum, my question is given a list of pathways and a set of genes, does anyone have some suggestion on how to highlight those genes (upregulated and downregulated with different colors) in the pathways I'm interested?

You can try genemania, either the web interface or (better) the Cytoscape plugin

HTH

[czc]

I like the Bioconductor SPIA package.

Thanks a lot. I'll try the package right now.

[czc]

You can try genemania, either the web interface or (better) the Cytoscape plugin

HTH

Thanks. I noticed the web interface before. Maybe I have not explored the function sufficiently. I'll try it later.