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Open AccessJournal ArticleDOI

Dysregulation of Gene Expression in the 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioned Mouse Substantia Nigra

TLDR
Microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration and disclosed dysregulation of genes in three main areas related to neuronal function.
Abstract
Parkinson's disease pathogenesis proceeds through several phases, culminating in the loss of dopaminergic neurons of the substantia nigra (SN). Although the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of oxidative SN injury is frequently used to study degeneration of dopaminergic neurons in mice and non-human primates, an understanding of the temporal sequence of molecular events from inhibition of mitochondrial complex 1 to neuronal cell death is limited. Here, microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration. This approach enabled the identification of small, yet consistently significant, changes in gene expression within the SN of MPTP-treated animals. Such an analysis disclosed dysregulation of genes in three main areas related to neuronal function: cytoskeletal stability and maintenance, synaptic integrity, and cell cycle and apoptosis. The discovery and validation of these alterations provide molecular evidence for an evolving cascade of injury, dysfunction, and cell death.

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Citations
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Journal ArticleDOI

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Leming Shi, +136 more
- 01 Sep 2006 - 
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Journal ArticleDOI

Synuclein activates microglia in a model of Parkinson’s Disease

TL;DR: The data suggest an early role for SYN and inflammation in PD pathogenesis, and evidence that the CD36 scavenger receptor and downstream kinases are involved in SYN-mediated microglial activation is provided.
Journal ArticleDOI

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

TL;DR: The results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs and recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists.
Journal ArticleDOI

Rat toxicogenomic study reveals analytical consistency across microarray platforms

TL;DR: The real-world toxicogenomic data set reported here showed high concordance in intersite and cross-platform comparisons and gene lists generated by fold-change ranking were more reproducible than those obtained by t-test P value or Significance Analysis of Microarrays.
Journal ArticleDOI

Gene expression profiling of substantia nigra dopamine neurons: further insights into Parkinson's disease pathology

TL;DR: Laser microdissection is used to isolate single DA neurons from the substantia nigra pars compacta of controls and subjects with idiopathic Parkinson's disease matched for age and postmortem interval followed by microarrays to analyse gene expression profiling, which provide a 'molecular fingerprint identity' of late-stage Parkinson's Disease DA neurons that will advance understanding of the molecular pathology of this disease.
References
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Journal ArticleDOI

Significance analysis of microarrays applied to the ionizing radiation response

TL;DR: A method that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements is described, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation.
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Summaries of Affymetrix GeneChip probe level data

TL;DR: It is found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models.
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Chronic Parkinsonism in humans due to a product of meperidine-analog synthesis

TL;DR: It is proposed that this chemical selectively damages cells in the substantia nigra in patients who developed marked parkinsonism after using an illicit drug intravenously.
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Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

TL;DR: A statistical model is proposed for the probe-level data, and model-based estimates for gene expression indexes are developed, which help to identify and handle cross-hybridizing probes and contaminating array regions.
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The ubiquitin pathway in Parkinson's disease

TL;DR: It is shown that in a German family with Parkinson's disease a missense mutation in the ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) gene causes a partial loss of the catalytic activity of this thiol protease, which could lead to aberrations in the proteolytic pathway and aggregation of proteins.
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The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

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