The inference capability of our refined computational framework is verified by various analyses including gene set enrichment analysis (GSEA), binding site enrichment analysis (BSEA), and additional literature survey.
Differential gene expression was performed including gene set enrichment analysis (GSEA) using publicly available breast cancer gene expression data sets.
An included gene set enrichment analysis provides an overview on the entities that might link the significant sites.
Further SAFE analysis, including gene set sizes >100, showed that only neurodegenerative diseases (4 out of 34 disease pathways) including ALS were significantly upregulated.
Where possible, MR-GSE is used with moderated t-statistics rather than ordinary t-statistics, as these are preferable for microarray analysis including gene set testing [ 56, 58].
Confero includes a local database for storage and management of data and metadata as well as tools for downstream computational analysis and biological interpretation, including gene set enrichment analysis (GSEA) and over-representation analysis (ORA) [ 17].
Both HK and tissue-specific genes were subjected to a comprehensive, three-phase functional analysis, including gene set enrichment across four ontologies, network topology analysis and tissue-specific network analysis.
A better solution would be to consolidate the complete list of pathways as non-redundant and representative pathways, enabling better understanding of any experiment including gene set enrichment results.
The first group includes gene sets related to "upstream" biological processes or genes for IGF-1.
This database also includes gene sets contributed by individual researchers and other similar databases such as the List of List Annotated (L2L) database [ 8].
