looking for tools to study additive expression effects in gene pathways/networks
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@christopher-t-gregg-4973
Last seen 7.1 years ago
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 [[alternative HTML version deleted]]
Pathways Rgraphviz KEGGgraph Pathways Rgraphviz KEGGgraph • 639 views
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