Filename D2.2 Data optimisation, enrichment, and preparation for analysis.docx Abstract: The intermediate data produced using various ETL pipelines during their development may not be consistent with the RDF Data Cube Vocabulary and the OpenBudgets.eu data model. This is why we developed several techniques for data optimisation, detecting such inconsistencies and reporting them to the pipeline ...

Gene set enrichment analysis (GSEA) is typically based on tests derived from the KolmogorovSmirnov, which is underpowered and a need for simpler methods has been identified.[2] The wgsea package contains functions for conducting GSEA using a Wilcoxon test to test for differences in the distribution of p values between SNPs within the gene set under test and a control set of SNPs. The mean of th...

The analysis of phosphopeptides can be particularly challenging since they are mostly present at very low concentrations in a complex proteolytic sample. Selective enrichment strategies have been introduced to capture phosphopeptides from the sample prior to MS analysis, which can enhance detection capabilities. One of the more successful phosphopeptide enrichment techniques is based on the sel...

Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valu...

Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of "significant genes." One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the se...

SUMMARY Systematically extracting biological meaning from omics data is a major challenge in systems biology. Enrichment analysis is often used to identify characteristic patterns in candidate lists. FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins. The novel tool FungiFun2 uses a completely revised data management system and thus allows enric...