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E-GEOD-33000 - Gene expression profiles of human prefrontal cortex brain tissues

Status
Released on 31 July 2014, last updated on 19 February 2019
Organism
Homo sapiens
Samples (1248)
Array (1)
Protocols (7)
Description
Dissecting the shared etiology of different diseases could benefit from a systematic search for associated molecules and their interactions. We investigated genome-wide disruptions in the co-regulation of genes in two neurodegenerative diseases, Alzheimer's or Huntington's disease (AD or HD), using expression profiles from postmortem prefrontal cortex samples of 624 demented patients and non-demented control individuals with matched genotype and clinical data. A meta-analysis based screen for changes in coordinate expression patterns revealed differentially co-expressed (DC) gene pairs that either gained or lost correlation in disease cases relative to the control group, with the former being dominant for both AD and HD. Integration of disruptions common to AD and HD with large-scale data on protein-protein and protein-DNA interactions yielded a 242-gene sub-network that was enriched for proteins involved in neuronal differentiation and genetic associations to brain structural changes and dementia in subjects aged over 70 years. Replication of the AD DC network in independent human and mouse cohorts lends confidence to the comprehensive view we offer on dysregulated brain molecular pathways in AD and HD. DLPFC (BA9) brain tissues of AD patients, HD patients and non-demented controls samples were obtained from Harvard Brain tissue resource center (HBTRC). The HBTRC samples were primarily of Caucasian ancestry, as only eight non-Caucasian outliers were identified, and therefore excluded for further analysis. Post-mortem interval (PMI) was 17.8+8.3 hours (mean ± standard deviation), sample pH was 6.4±0.3 and RNA integrity number (RIN) was 6.8±0.8 for the average sample in the overall cohort. Tissues were profiled on a custom-made Agilent 44K array (GPL4372). 624 individual DLPFC samples were profiled against a common DLPFC pool constructed from the same set of samples.
Experiment type
transcription profiling by array 
Contacts
Jun Zhu <junzhu_99@yahoo.com>, Bin Zhang, Christine Suver, Chunsheng Zhang, Cliona Molony, David J Stone, Eric E Schadt, John R Lamb, Joshua McElwee, Kai Wang, Manikandan Narayanan, Stacey Melquist, Tao Xie, Valur Emilsson, Xia Yang
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-33000.idf.txt
Sample and data relationshipE-GEOD-33000.sdrf.txt
Processed data (2)E-GEOD-33000.processed.1.zip, E-GEOD-33000.processed.2.zip
Additional data (1)E-GEOD-33000.additional.1.zip
Array designA-GEOD-4372.adf.txt
Links