DATASETS CURRENTLY AVAILABLE
We have partnered with the WPIC Office of Academic Computing to develop three databases: MDD Effect, Age Effect and Relative Enrichment in Transcript Cellular Origin (a hyperlink to each database appears below). In line with the NIH requirement to make large-scale transcriptome data available to the broader scientific community, we invite student and professional researchers to interrogate our datasets for genes of interest.
- Meta-analysis of altered gene expression in major depression
- Age Effect on Gene Expression Levels in the Human Brain
- Relative Enrichment in Neuronal/Glial Origin of Gene Transcript
Interactive Database for Meta-analysis of altered gene expression in major depression
Interactive Database for Age Effect on Gene Expression Levels in the Human Brain
Interrogate this dataset for changes in gene expression correlating with age in the human brain.
This database provides access to large-scale gene expression data from two different cohorts across four areas of the human brain: prefrontal cortex BA9, prefrontal cortex BA47, anterior cingulate cortex, and amygdala. This tool is designed to be used freely and publicly by any researcher interested in gene function in the human brain in the context of aging or neuropsychiatric disorders.
Support for the generation of primary data was provided by NIH, NIMH, and the University of Pittsburgh Institute on Aging.
Details in: Erraji-Benchekroun L, Underwood MD, Arango V, Galfalvy H, Pavlidis P, Smyrniotopoulos P, Mann JJ, Sibille E. Molecular aging in human prefrontal cortex is selective and continuous throughout adult life. Biol Psychiatry. 2005 Mar 1;57(5):549-58. PubMed PMID: 15737671.
Details in: Glorioso C, Oh S, Douillard GG, Sibille E. Brain Molecular Aging, Promotion of Neurological Disease and Modulation by Sirtuin5 Longevity Gene Polymorphism. Neurobiology of Disease. Accepted 2010.
Interactive Database for Relative Enrichment in Neuronal/Glial Origin of Gene Transcript
Ratios of gene transcript levels between gray and adjacent white matter samples can be used to estimate the relative glial/neuronal cellular origins of expression.
For every gene in each brain area, two average signal intensities were calculated: one average value using all gray matter (GM) samples collected in that area, and one average value using all white matter (WM) samples collected nearby. A ratio was then calculated between these two average values for each gene, representing the WM/GM ratio of gene transcript for that gene in that particular brain area. [Support for the generation of primary data was provided by NIH and NIMH.]
WM/GM Fold change >1.5 corresponds to relative glial enrichment
WM/GM Fold change <-1.5 corresponds to relative neuronal enrichment
-1.5< WM/GM < 1.5 indicates equal representation of glial and neuronal origin of transcript
Details in: Sibille et al. Large-scale estimates of cellular origins of mRNAs: Enhancing the yield of transcriptome analysis. J Neurosci Methods. 2008 Jan 30;167(2):198-206. Epub 2007 Aug 21. PubMed PMID: 17889939. PMCID: PMC2262176. Please cite this reference.