PROMPT

PROMPT integrates and analyzes molecular biology data from heterogeneous molecular biological databases and custom XML formats to enable identifier mapping, statistical comparison, enrichment analysis, and numeric correlation across protein datasets.

Key Features:

• Automatic data retrieval: Retrieves data automatically from various molecular biological databases and custom XML formats.
• Similarity-based identifier mapping: Performs similarity-based mapping of sequence identifiers to reconcile gene identifier discrepancies and minor sequence variations.
• Categorical frequency comparison: Compares frequencies of categorical annotations between two protein sets.
• Enrichment analysis: Assesses enrichment of nominal features within one set relative to another.
• Numeric distribution analysis: Analyzes numeric distributions across datasets.
• Correlation analysis: Computes correlations between numeric variables to identify significant relationships.
• Result export: Produces plots and spreadsheets and supports exporting results in various formats, including Microsoft Excel.

Scientific Applications:

• Data integration: Integrates disparate experimental information from multiple molecular biological databases and custom XML sources.
• Identifier reconciliation: Links experimental data across sources by mapping sequence and gene identifiers despite discrepancies.
• Annotation comparison: Compares categorical annotations and tests for enrichment between protein sets.
• Quantitative analysis: Evaluates numeric feature distributions and identifies correlations among numeric variables within and between datasets.

Methodology:

Automatic data retrieval from molecular biological databases and custom XML; similarity-based mapping of sequence identifiers to reconcile gene identifier and sequence discrepancies; statistical procedures including categorical frequency comparison between two protein sets, enrichment assessment of nominal features, numeric distribution analysis, and correlation of numeric variables; generation of plots, spreadsheets, and exports including Microsoft Excel.