How data was processed:
One of the aims of Interferome DB is to provide the storage and analysis of gene expression data obtained from microarray experiments of interferon treated cells or animals.
Microarray datasets were manually selected from EBI Array express, GEO open sources DBs and in-house experiments. Selection criteria are variety cells or tissues treated with any type of interferon (IFNs), with or without other treatments. The cells/tissues/enimals could be normal or abnormal (for example, originating from a diseased organism or one with a genetic modification).
Data was collected from various microarray platforms and array designs. In relation to each platform normalization and filtering algorithms was applied, such as RMA, GCRMA, MAS5, Percentile.
The microarray server runs BioArray Software Environment (BASE 2) for the storage, management and analysis of microarray experiments. BASE2 use plug-ins for data analysis which provides also data normalization, transformation and filtering. Statistical analysis of technical and biological replicates of experimental samples includes Welch t-test and Fold change calculations. Analysis is performed using the BASE2 platform and the Bioconductor packages.
The outcome of the analyses from BASE2 is presented in Interferome ‘Search - Experiment Data’ page as a list of statistically significant genes (p-value < 0.05) with fold change expression between treated and untreated samples.
The data is also annotated for various parameters including type of IFN, concentration, time of treatment, cell type and normal/abnormal status and others.
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