OSCAR

OSCAR performs clustering and cross-species analysis of microarray data to identify co-regulated gene clusters and conserved expression patterns across species.

Key Features:

• Supported data: Analysis of microarray data including single-species and cross-species datasets.
• Clustering algorithms: Implements Hierarchical Clustering, K-means, Partition Around Medoids (PAM), Self-Organizing Map (SOM), Tight Clustering, and Consensus Tight-clustering.
• Consensus Tight-clustering: A variant reported to produce gene clusters that are more resistant to false positives compared to other algorithms.
• Cross-species algorithms: Provides coherentCluster and coherentSubset for detecting conserved co-regulation across species.
• Visualization: Includes a comparative heatmap for visualization of cross-species expression patterns.
• Algorithm integration: Supports integration of external algorithms as command-line executables without requiring source code disclosure.

Scientific Applications:

• Single-species clustering: Identification of gene clusters and co-regulated gene sets within a single organism's microarray data.
• Cross-species conservation: Detection of conserved co-regulated gene clusters between species, exemplified by human and Drosophila comparisons.
• Aging-related discovery: Applied to human and fly aging datasets to identify gene clusters with co-regulation patterns correlated with aging.
• Regulatory pathway hypothesis: Supported identification of a putative INSR -> Pax6 -> NQO1 detoxification neuro-protective pathway relevant to aging or diseased brains.
• Integration with pathology: Enables analysis combining human brain expression data and pathological data to explore disease-related expression patterns.

Methodology:

Uses Hierarchical Clustering, K-means, PAM, SOM, Tight Clustering and Consensus Tight-clustering; applies coherentCluster and coherentSubset for cross-species analysis; generates comparative heatmaps; has been applied to human and Drosophila aging microarray datasets and to integrated human brain expression and pathological data.