GOseq

GOseq performs Gene Ontology (GO) enrichment and depletion analysis for RNA-seq differential expression results by using a statistical framework that accounts for transcript length and abundance to correct RNA-seq-specific bias.

Key Features:

• RNA-seq specificity: Tailors GO analysis to RNA-seq datasets rather than methods developed for other expression platforms.
• Statistical framework: Incorporates a statistical framework that explicitly accounts for transcript length and abundance.
• Bias correction: Adjusts for the over-detection of differential expression among long and highly expressed transcripts.
• GO enrichment/depletion assessment: Provides assessments of Gene Ontology category enrichment or depletion in differential expression results.
• Biological concordance: Alters GO analysis outcomes to highlight GO categories that better align with established biological knowledge.

Scientific Applications:

• RNA-seq differential expression studies: Applied to identify enriched or depleted GO categories from RNA-seq-derived gene lists.
• Prostate cancer datasets: Demonstrated to significantly change GO analysis results in prostate cancer studies, highlighting biologically relevant GO categories.

Methodology:

Implements a statistical framework that models and adjusts for transcript length and abundance when testing Gene Ontology category enrichment or depletion to correct RNA-seq-specific biases.