PageMan

PageMan provides analysis and visualization of high-throughput microarray data within functional ontologies to identify and compare genome-level functional responses.

Key Features:

• Functional Ontology Integration: Annotates microarray data within functional ontologies and supports transformation and selection of multiple ontology formats.
• Statistical Analysis Modules: Performs over-representation analysis and Wilcoxon statistical testing to identify significant functional patterns.
• Graphical Data Exportation: Exports analysis results in graphical formats for downstream presentation and external customization.
• Comparative Analysis Capabilities: Generates rapid genome-level comparisons across multiple microarray experiments, including stress responses at various time points, trait-specific pathway changes in mutants or transgenics, developmental time-course analyses, and interspecies comparisons.

Scientific Applications:

• Large-scale time-course and genetic-variation studies: Supports analysis of experiments involving multiple time points or genetic variants using microarray data.
• Data condensation and visualization: Condenses and visualizes results from multiple microarray experiments onto a single graphical display for rapid interpretation.
• Comparative stress and mutant/transgenic analyses: Enables comparison of stress-response profiles and trait-specific pathway changes in mutants or transgenics.
• Developmental and interspecies comparisons: Facilitates developmental time-course analyses and comparisons between species at the genome-function level.
• Meta-analysis and validation (cold stress case study): Applied to publicly available cold stress microarrays and compared with previously published meta-analyses for validation and expansion of findings.

Methodology:

Annotation of microarray data to functional ontologies with transformation/selection of ontology formats, over-representation analysis, Wilcoxon statistical testing, graphical export of results, and genome-level comparisons across experiments.