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Pers, T. H. Gene set analysis for interpreting genetic studies.
Yaari, G., Bolen, C. R., Thakar, J. & Kleinstein, S. H. Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.
The MAVTgsa package performs a systematic gene set analysis for identification of different types of gene set significance modules.
Gene set analysis for FL-interacting genes resulted in individual AUC%s for each ET experiment, which were plotted for each of the 6 gene sets as shown in Figure 5.
Therefore, these CoGAPS expression signatures reveal degrees of activation of the pathways downstream of EGFR due to pathway cross-talk, unlike the standard gene set test or permutation gene set analysis for linear models.
The same pattern of strong differences between blastomeres and ICM and TE samples and of weak differences among blastomeres was found in the Gene Set Analysis for the Gene Ontology terms and the KEGG pathways using the Babelomics functional profiling tools (see Methods).
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Gene ontologies have been used in many ways for the quantitative analysis of gene expression profiles, for gene set analysis and for general annotation analyses [ 9- 11].
However, for the gene set analysis and for the analysis of the merged datasets separate channel intensities were needed.
Within the last few years, multiple approaches for gene set analysis have been proposed for both expression and SNP data.
We propose a novel gene set analysis specifically designed for gene sets defined by pathways.
One of the motivations for doing set analysis is to uncover signals for such regions.
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