High-throughput techniques gives us a list of differentially or co-expressed genes. Now, which methods can infer a pathway from a list of genes (static or dynamic pathways)? How do they work?
Dear Sadeg,
this article can be useful:
"Ten years of pathway analysis: current approaches and outstanding challenges."
by Khatri P, Sirota M, and Butte AJ (PLoS Comput Biol. 2012). It´s freely available so just follow the link: http://www.ncbi.nlm.nih.gov/pubmed/22383865
Cheers
Dear Thomas
I have studied several papers and several chapters before.
The best was "Statistical Methods for Pathway Analysis of Genome-Wide Data for Association with Complex Genetic Traits"
But those software that also you have mentioned are included in. I couldn't find good review paper about statistical picture of these software.
Dear Sadeg,
this article can be useful:
"Ten years of pathway analysis: current approaches and outstanding challenges."
by Khatri P, Sirota M, and Butte AJ (PLoS Comput Biol. 2012). It´s freely available so just follow the link: http://www.ncbi.nlm.nih.gov/pubmed/22383865
Cheers
Take a look at Reactome (http://reactome.org), a free, open-source, curated and peer reviewed pathway database. You will find intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.
And we are always available to help.
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