SPEX2

SPEX2 processes in situ hybridization (ISH) images of Drosophila embryos to extract spatial locations and strengths of mRNA expression for comparative, clustering, and functional analyses.

Key Features:

• Automatic Image Processing: Automates processing of in situ hybridization (ISH) images.
• Pattern Extraction and Transformation: Extracts precise spatial locations and expression strengths and transforms raw image data into analyzable formats.
• Comparison, Classification, and Clustering: Compares, classifies, and clusters spatial gene expression patterns.
• Functional Annotation Enrichment: Identifies clusters significantly enriched for Gene Ontology functional annotations and terms from controlled vocabularies used by human curators.

Scientific Applications:

• Functional Genomics: Enables mining of temporal-spatial mRNA patterns to associate genes with biological functions via cluster analysis and annotation enrichment.
• Network Inference: Supports inference of gene interaction networks by comparing and clustering spatial expression patterns.
• Embryonic Development Studies: Facilitates analysis of gene expression dynamics during Drosophila embryonic development using ISH image collections.

Methodology:

Processes large collections of Drosophila ISH images via automatic image processing, extracts spatial locations and expression strengths, transforms images into analyzable data formats, performs comparison, classification and clustering of spatial patterns, and conducts enrichment analysis using Gene Ontology and controlled-vocabulary curator terms.