CLEAN

CLEAN quantifies gene-level functional coherence within cluster analyses to incorporate predefined functional gene categories into the interpretation of genomics datasets.

Key Features:

• Gene-Specific Functional Coherence Score (CLEAN Score): A gene-level metric that quantifies functional coherence by correlating the overall clustering structure with predefined functional categories.
• Integration of Biological Knowledge: Incorporates lists of functionally related genes as predefined functional categories into cluster analysis to assess coherence at the gene level.
• R Implementation: Provides routines implemented in an R package for calculating gene-specific functional coherence scores.
• Improved Reproducibility and Informative Output: Identifies genes with functionally coherent expression profiles and improves reproducibility of conclusions across independent genomic datasets.
• Comparative Analysis: Supports comparison of clustering results produced by various clustering algorithms to evaluate and contrast clustering outcomes.

Scientific Applications:

• Genome-wide functional genomics studies: Interprets clustering results in the context of predefined functional gene categories across genome-scale datasets.
• Pathway and process identification: Aids identification of pathways and biological processes associated with specific biological conditions or treatments.
• Disease biomarker discovery: Helps prioritize genes with coherent functional expression profiles relevant to disease states.
• Drug target identification: Supports identification of candidate targets by linking clustered gene expression patterns to functional categories.
• Systems biology: Facilitates functional interpretation of networked or modular gene expression patterns within systems-level analyses.

Methodology:

Compute the CLEAN score by correlating overall clustering structure with predefined functional categories; integrate lists of functionally related genes into cluster analysis; implement routines to calculate gene-specific functional coherence scores and compare clustering results across algorithms.