Hi,

We are seeking recommendations for approaches to study how gene expression effects may become additive within pathways.  We have logFC values for genes differentially expressed in a comparison of control to treatment.  We are interested in the following problem: 

Genes A and B exhibit a modest increase in expression of 1.5 fold each and exist in the pathway A->B->C.  Therefore, we expect the effects of the expression changes for A and B to become additive, yielding a net effect on C that is increased by 3-fold compared to baseline.  We wish to identify, visualize and study these scenarios within KEGG annotated pathways.

I expect that this sort of analysis is implemented in software intended to study complex networks, but can't see it obviously available in Rgraphviz or KeggGraph, for example.  Expert advice would be greatly appreciated.

Thank you.

best wishes,
Chris


Christopher Gregg, PhD.
New York Stem Cell Foundation-Robertson Investigator
Assistant Professor, Neurobiology and Anatomy
Adjunct Assistant Professor, Human Genetics
323 Wintrobe Bldg 530
University of Utah, School of Medicine
20 North 1900 East
Salt Lake City, Utah 84132-3401

phone: (801) 581-8212
fax: (801) 585-9736
------------------------------------
Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html



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