Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human substantia nigra from postmortem brain of Parkinsons disease patients (PD)

ABSTRACT: We used microarrays to detail the global program of gene expression underlying Parkinson's disease Experiment Overall Design: Substantia nigra tissue from postmortem brain of normal and Parkinson disease patients were used for RNA extraction and hybridization on Affymetrix microarrays: 9 replicates for the controls and 16 replicates for the Parkinson's disease patients were used. Both cohorts included males and females.

ORGANISM(S): Homo sapiens

SUBMITTER: Jarlath ffrench-Mullen

PROVIDER: E-GEOD-7621 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

Lesnick Timothy G TG Papapetropoulos Spiridon S Mash Deborah C DC Ffrench-Mullen Jarlath J Shehadeh Lina L de Andrade Mariza M Henley John R JR Rocca Walter A WA Ahlskog J Eric JE Maraganore Demetrius M DM

PLoS genetics 20070601 6

While major inroads have been made in identifying the genetic causes of rare Mendelian disorders, little progress has been made in the discovery of common gene variations that predispose to complex diseases. The single gene variants that have been shown to associate reproducibly with complex diseases typically have small effect sizes or attributable risks. However, the joint actions of common gene variants within pathways may play a major role in predisposing to complex diseases (the paradigm of ...[more]

PMID: 17571925

Similar Datasets

Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD)

Project description:We used microarrays to detail the global program of gene expression underlying Parkinson's disease Keywords: normal versus diseased

2007-06-14 | GSE7621 | GEO

Gene expression profiling of parkinsonian substantia nigra

2010-03-10 | GSE20333 | GEO

Transcriptional analysis of whole substantia nigra in Parkinson's disease

Project description:Post mortem tissue was dissected from two groups of age and gender matched groups of Parkinson and Control subjects Published work contains more information on Parkinson and Control groups

2010-03-23 | E-GEOD-20292 | biostudies-arrayexpress

Transcriptional analysis of whole substantia nigra in Parkinson's disease

Project description:Post mortem tissue was dissected from two groups of age and gender matched groups of Parkinson and Control subjects

2010-03-12 | GSE20292 | GEO

Age-mediated transcriptomic changes in adult mouse substantia nigra

Project description:Substantia nigra pars compacta (SNpc) is highly sensitive to normal aging and selectively degenerates in Parkinson's disease. Until now, molecular mechanisms behind SNpc aging have not been fully investigated using high throughput techniques. Here, aging-associated early changes in transcriptome of SNpc were investigated comparing late middle-aged (18 months old) to young (2 months old) mice.

2013-05-29 | GSE45043 | GEO

Transcription profiling of human Parkinsons medial and substania nigra

Project description:Affymetrix HG_U133 array sets (A and B chips) were used to determine the whole genome transcription profile of clinically documented and neuropathologically confirmed cases of sporadic Parkinson's disease as well as controls. Experiment Overall Design: Post mortem brain tissue samples from Parkinson's disease and control cases (substantia nigra, split into medial and lateral portions, and frontal cortex) were prepared for this study. In total, 47 individual tissue samples were analyzed using one A and one B GeneChip per sample, i.e. 15 samples of medial parkinsonian SN, 9 samples of lateral parkinsonian SN, 8 medial nigra control samples and 7 lateral nigra control samples. Lateral and medial nigra samples were from the same cases. In addition, frontal cerebral cortex was analyzed in five of the PD cases and in three of the controls (Neurogenetics 2006 7: 1â??11; Acta Neuropathologica (Berlin) 2007 113: 253-263

2008-06-16 | E-GEOD-8397 | biostudies-arrayexpress

Gene expression in Parkinson modeled mouse substantia nigra pars compacta at single cell resolution

Project description:Strong evidence in human populations indicates that pesticide exposure increases the risk of Parkinson's disease . However, to date there has no study investigating the role of genetic pathways for pesticide induced PD at cellular resolution. We used single cell RNA sequencing to provide fine-grained information on the genetic pathways of Parkinson's disease caused by a combined regimen of maneb and paraquat. We investigated the substantia nigra pars compacta of control mice and mice treated with maneb and paraquat to identify changes in gene expression in cellular subpopulations such as neurons, glia and vascular cells. This work reveals how neuronal and non-neuronal cells interact in the context of a toxicologically and environmentally relevant model Parkinson's disease, while offering entry points to the design of new therapies.

2021-11-03 | GSE187012 | GEO

Gene expression profiling of parkinsonian substantia nigra

Project description:Affymetrix HG-Focus array was used to determine a global gene expression profile of clinically and neuropathologically confirmed cases of sporadic Parkinson's disease compared to controls. Major alterations were detected in signal transduction, protein degradation, dopaminergic transmission/metabolism, energy pathways/glycolysis, cell adhesion/cytoskeleton, extracellular matrix components and cell cycle functional classes. Post-mortem human brains were obtained from moderately to severe parkinsonism individuals based on the Hoehn & Yahr criteria. All the subjects were negative for AD pathology according to Braak & Braak. The average age for PD and control is 76.6 and 77.8 years, respectively. The average postmortem delay for PD and control is 26.2 and 19.8 hours, respectively.

2010-03-23 | E-GEOD-20333 | biostudies-arrayexpress

Gene expression profiling of substantia nigra: a post-mortem study in Parkinson's disease and control subjects

Project description:Introduction: Parkinson's disease (PD) is characterized by bradykinesia, tremor, and rigidity; in addition, postural instability sets in as the disease progresses. Non-motor symptoms of the disease include cognitive, behavioral, and neuropsychiatric changes, sensory and sleep disturbances that may precede the motor symptoms of the disease itself. The peculiar pathological features of PD are decreased dopaminergic neurons and dopamine levels in the substantia nigra pars compacta and pontine locus ceruleus. The study of the transcriptome plays a major role in the identification of genes and gene regulatory mechanisms in multifactorial neurodegenerative diseases such as Parkinson's disease itself. Therefore, we proposed to study the transcriptome directly in the midbrain containing the "Substantia nigra.The study was performed in 8 subjects with PD and 6 normal control subjects, using next-generation sequencing (NGS) technologies. Results: With the use of an ad hoc bioinformatics pipeline, gene expression profiles in the different PD subjects were obtained and compared to those of controls. In detail, the results obtained from the data analysis indicated 92 differentially expressed genes (FDR-adjusted p value ≤0.05 and fold-change less than -1.5 or greater than +1.5) of which 33 genes were up-regulated while 59 were down-regulated. Conclusions: Functional analysis of the differentially expressed genes revealed several genes involved in different canonical pathways indicating their likely significant role in Parkinson's disease.

2024-01-03 | E-MTAB-13295 | biostudies-arrayexpress