A cross-laboratory comparison of expression profiling data in the human postmortem brain

Supplement to A cross-laboratory comparison of expression profiling data from normal human postmortem brain.
Mistry M, Pavlidis P pubmed reprint

Abstract

Background: Expression profiling of post-mortem human brain tissue has been widely used to study molecular changes associated with neuropsychiatric diseases as well as normal processes such as aging. Changes in expression associated with factors such as age, gender or postmortem interval are often more pronounced than changes associated with disease. Therefore in addition to being of interest in their own right, careful consideration of these effects are important in the interpretation of disease studies.

Methods: We performed a large meta-analysis using 11 genome-wide expression studies of normal human cortex to more fully catalogue the effects of age, gender, postmortem interval and brain pH, yielding a “meta-signature” of gene expression changes for each factor. We validated our results by comparing signature genes for each factor with the literature.

Results: Our meta-signatures show a significant overlap with independent gene lists extracted from the literature. Importantly, we observe genes in the profiles are only identified through meta-analysis. We also show that many schizophrenia candidate genes appear in the meta-signatures, reinforcing the idea that studies must be carefully controlled for interactions between these factors and disease.

Conclusions: In addition to the inherent value of the meta-signatures, our results provide critical information for future studies of disease effects.

Contact

paul@chibi.ubc.ca

Supplementary Files

Full Manuscript

 

Supplementary Figures

Supplementary Text and Tables
Supplementary Table 5
Supplementary Table 6
Supplementary Table 7

 

R Code

 

Additional Analyses