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Parkinson's disease database

(Last Update: December 16th 2010)

Aim

The Parkinson's Disease Database is a gene expression database which allows the user to mine data collected from ArrayExpress experiments across several clinical samples and animal models.
This database contains a subset of curated and re-annotated datasets which can be queried for individual gene expression under different biological conditions across experiments and across different organisms.
The data in ArrayExpress is imported from GEO if it passes ArrayExpress QC. The database refers to experiments through their GEO numbers in the format of E-GEOD-n, see http://www.ebi.ac.uk/microarray/doc/help/faq.html#query_FAQ

Data Mining

Using the menu above users can query for:
  • GENES: It shows differential expression analysis results across experiments and different organisms for specific genes of interest.
  • EXPERIMENTS: It shows all the genes that are differentially expressed in specific experiments.
  • TISSUES: It shows the experiments related to the selected tissue and the differentially expressed genes relating to those specific contrasts.
  • COMPARISON: This page allows the user to obtain the common genes that are differentially expressed in different experiments. This query supports also cross-organism comparisons, using orthology information retrieved from Ensembl database.
  • DOWNLOADS: This page allows the user to download raw data files for each experiment.

Statistics

All the experiments were re-analyzed utilizing the rma normalization method, a linear transformation and a Bayesian t test using the LIMMA package.
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