… gene set analysis approaches and tools by the type of genomic study, null hypothesis,
sampling model and nature of the test statistic, etc. Rather than reviewing the gene set analysis …

… within the hypothesis testing context via permutation tests [219]. Permutation tests express a
… under the null (arbitrary) hypothesis from the offered data. The estimation of the probability …

… After pre-analysis, the methods perform differential analysis at the gene-level and then
identify significant pathways using statistical hypothesis testing. The output often includes …

… data mining warehouse for querying and exporting disparate sources of gene annotation
data… that can be used with GeneMerge, a command-line GO enrichment software package (67). …

… data sets and 121 samples from 11 knockout mouse data sets. In addition, we investigate
the extent to which each method is biased under the null hypothesis. Together, these data and …

… tool to provide statistically rigorous hypothesis testing, a clear illustration of the Gscore
procedure, and intuitive and interactive visualizations of findings. In summary, Gscore offers a …

… their gene score, null hypotheses, and essential evaluation methods. The authors believe
that a standardized approach for testing the methods of gene set analysis can also be used for …

… Then, they compute the probability of observing a certain number of altered genes in a
pathway by chance applying a hypothesis test [24]. However, these methods have several …

… Therefore we discuss various aspects of the GSA with QTLs, such as null hypothesis, sampling
model, and nature of the test statistic, for interpreting high-throughput GE data in context …

… As such, these modules serve as tools for generating new testable hypotheses, including
the prediction of gene function and importance. Recently, we have seen a paradigm shift from …