categoryCompare

categoryCompare compares annotation-level results from high-throughput omics datasets to identify shared and distinct biological annotations across measurement platforms.

Key Features:

• Annotation-Level Comparison: Assesses annotations (e.g., known or predicted functions and associations) of features to enable cross-platform and cross-sample comparison of biological processes and signaling pathways.
• Significance Calculation and Overlap Detection: Calculates significant annotations for each feature list (e.g., gene lists) and determines overlaps between these annotations, with graphical and tabular outputs illustrating annotation combinations across lists.
• RCytoscape Integration: Exports annotation networks compatible with RCytoscape for network visualization.
• Platform Heterogeneity Handling: Uses annotation-level analysis to evaluate common biological processes across studies even when individual features are not consistently measured.

Scientific Applications:

• Denervated Skin vs. Denervated Muscle: Comparison of annotation-level responses to reveal distinct tissue-specific biological reactions.
• Crohn’s Disease vs. Ulcerative Colitis (UC): Identification of shared inflammatory responses and processes unique to each condition from annotation-level analyses.

Methodology:

Calculates significant annotations per feature list and determines annotation overlaps; assesses utility using hypothetical and real datasets; analytical factors explicitly considered include number of genes per annotation term, noise levels in unenriched categories, and methods for combining samples.