topGO

topGO is a software package for enrichment analysis of Gene Ontology (GO) terms using gene expression data. Its main goal is to improve the scoring of functional gene groups by taking into account the hierarchical structure of the GO graph.

Key points:

1. topGO addresses the issue of dependencies between GO terms due to the hierarchical nature of the GO graph, which can lead to redundant and misleading results in traditional enrichment analysis methods.

2. The package implements two novel algorithms, "elim" and "weight," which use the GO graph topology to decorrelate the GO terms and reduce local dependencies between them.

3. The "elim" algorithm iteratively removes genes mapped to significant GO terms from more general (higher level) GO terms. In contrast, the "weight" algorithm assigns weights to each gene based on the scores of neighboring GO terms.