ArrayXPath

ArrayXPath maps clustered microarray gene-expression profiles onto biological pathways to enable pathway-centered analysis and visualization of gene-pathway-disease-drug relationships.

Key Features:

• Input format: Accepts clustered gene-expression profiles in a tab-delimited text format derived from microarray experiments.
• Pathway integration: Maps microarray probe identifiers and gene-expression data onto known biological pathway elements.
• Database integration: Incorporates Gene Ontology (GO), Medical Subject Headings (MeSH), and OMIM Morbid Map annotations for contextualization.
• Correlation integration: Integrates correlations between genes, diseases, drugs, and pathways to provide a holistic view of interactions.
• Statistical analysis: Computes Fisher's exact test and relative risk and applies false discovery rate (FDR) corrections for multiple comparisons.
• Automated identifier mapping: Automatically maps various identifiers from microarray probes to pathway elements.
• Visualization technology: Produces Scalable Vector Graphics (SVG) visualizations with JavaScript-enabled interactivity to explore mapped data.

Scientific Applications:

• Pathway crosstalk analysis: Identifies and visualizes interactions between different biological pathways using mapped gene-expression data.
• Disease mechanism elucidation: Highlights disease-associated genes within pathways to support identification of potential biomarkers and targets using GO, MeSH, and OMIM annotations.
• Drug response analysis: Relates gene-expression changes to drug associations and pathway context to inform hypotheses about drug responses.

Methodology:

Maps tab-delimited clustered microarray gene-expression profiles to pathway elements, integrates GO, MeSH and OMIM Morbid Map annotations and gene/disease/drug/pathway correlations, automatically maps probe identifiers to pathway components, computes Fisher's exact test and relative risk with false discovery rate (FDR) correction, and generates SVG visualizations with JavaScript-enabled interactivity.