In addition to providing a data repository for a variety of pancreatic beta-cell experiments, the EuroDia database contains several analysis tools for mining the data. Through the web interface, a user can identify differentially expressed genes by fitting a linear model for each gene and evaluating the fold change and moderated t
). It is possible to use one of several web forms designed to describe common experimental set-ups; the different web forms available are for (i) group designs allowing to compare two or more conditions, (ii) factorial designs of type two by two for comparing the combined effect of two conditions or treatments (e.g. the combined effect of a treatment and a mutant background) or (iii) paired samples where hybridizations are compared by pairs. The latter may be used, for example, to identify differentially expressed genes between alpha and beta cells of six pancreas samples, each alpha cell sample being paired with the beta cell sample from the same organ. Radio buttons and checkboxes are used to assign each hybridization to a condition. A few additional filters can also be set to correct the obtained P
-values for multiple testing using either Holm, Benjamini-Hochberg or the Storey-Tibshirani false discovery rate (FDR) methods and to exclude probes showing low expression and/or variance. Results are presented as tables that can be sorted, filtered and downloaded together with probe annotations provided by the array manufacturer ().
Figure 2. Experiment analysis. The order of the boxes reflects the flow of analysis steps. From top to bottom and left to right, the experiment name and description, the selection of the type of analysis, the form to describe analysis design (for this example, (more ...)
Once a set of differentially expressed genes has been identified, the next step is often to explore the biology around these genes. The EuroDia database provides several tools to help extract valuable information and knowledge from gene expression data. From the web interface a user can evaluate whether the differentially expressed genes are enriched for particular gene ontology (GO) (12
) categories, KEGG pathways (13
) or Reactome metabolic maps (14
). The results are presented as a table of significant categories or pathways with the relevant P
-values for enrichment. In addition to these enrichment analyses, a user can also perform Gene Set Enrichment Analysis (GSEA) (14
) using ordered gene lists to identify enriched pathways or functionally related groups of genes. The gene lists for GSEA can either be selected from MSigDB (14
) or imported by the user.
As an alternative, for some experiments a user might be interested in identifying subgroups of genes and conditions that share similar expression profiles (expression modules). The EuroDia database interface offers the possibility to identify expression modules using the iterative signature algorithm (15–17
). For each expression module, a GO category, KEGG pathway and chromosomal location enrichment is computed (18
The EuroDia database contains datasets from different organisms and different microarray platforms. It is possible to combine multiple experiments of the same platform type (Affymetrix or spotted) by merging probes using either their unique probe identifier (to combine data from two versions of the same platform), NCBI gene index (to combine data from the same organism on different platforms) or NCBI homologene id (to combine data from different organisms). To address the problem of variability between measurements originating from different laboratories, expression ratios between conditions are not calculated for merged experiments. Instead, the rank products algorithm (20
) is used to compare the co-occurrence of one gene amongst the most up or down regulated genes of all the compared hybridizations.
Finally, to provide a more global view of the data, tools have been incorporated to display the expression profile of a particular gene across the whole database and to measure the correlation of the global expression profiles of two genes.