About us

Gene expression data were retrieved from ArrayExpress and/or GEO database. The current datasets are from both Affymetrix and cDNA platforms. Those datasets were: 1) categorized into our defined experimental class and sub-class and 2) curated for control (untreated) and case (treated) samples, according to their experimental condition. We performed two types of gene expression analysis: pairwise and meta- analysis and deposited the results in the database.
The Piano R package is used for computing differentially expressed genes and performing analyses of three different gene sets: gene ontology (GO), transcription factor (TF) and pathway (PTW). The metaMA R package is applied for meta-analysis which combines data from independent, but related studies. By using gene expression datasets of the same sub-class to calculate and combine moderated effect sizes from different studies we retrieve genes with significantly changed expression and obtain enriched gene sets of that specific sub-class.
For any further questions, suggestions, and feedback, please email us: dina.petranovic[at]chalmers.se


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Funding:


This project was supported by The Chalmers Foundation and BILS (Bioinformatics Infrastructure for Life Science).