Help wanted interpreting a pathway analysis table

Question

[barryfic]

Help would be greatly appreciated, and probably very easy for someone with knowledge in the field of pathway analysis.

I am at a loss as to how to interpret a table of pathway analysis in a study I'm reading. http://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0091006.t001 Does this mean the relative risk of Alzheimer's, Huntington's, and Parkinson's is increased or decreased, and to what extent? Thanks in advance.

Answer 1

[Steven Lakin]

They overexpressed this protein in transgenic mice, then did a comparison of the genes expressed in that overexpressed group vs. wild-type. They took the genes, classified them into known pathways, and what you're seeing in the table are the p-values associated with up-regulation (these pathways are more expressed in the transgenic mice than in WT).

You should interpret this as an implication that the overexpressed protein (PGC-1a) could be related to the gene expression/modulation of known Alzheimer's, Huntington's, and Parkinson's disease genes/gene pathways. It's an association, not relative risk; to get odds or relative risk, they would have to do a study in clinical cases.

[barryfic]

Thanks so much. Modulation would not seem to imply whether it is an increase or decrease in the disease/gene pathway, only that it is relative to said pathway.

I hesitate to read much into this research as it pertains to humans, as murine models seem poor representatives of human PPAR activity.

Thanks again.