GSE

GSE stores, retrieves, and analyzes diverse high-throughput microarray datasets to support analysis of ChIP-chip data, gene expression data, genomic annotations, and functional annotations across multiple species and genome builds.

Key Features:

• Data types: Manages ChIP-chip, gene expression, genomic annotation, and functional annotation datasets.
• Multi-species and genome-build support: Handles concurrent datasets from multiple species and different genome builds within a single species.
• GSEBricks framework: Implements the GSEBricks middle software layer to represent biological data streams and enable dataset integration and interaction.
• ChIP-chip visualization: Provides a Java-based visualization application for ChIP-chip analysis that communicates over a network with the GSE database.
• Joint Binding Deconvolution: Incorporates a published Joint Binding Deconvolution algorithm to deconvolve complex transcription factor binding events in ChIP-chip data.
• Binding hypotheses: Records and manages binding hypotheses that describe relationships between different ChIP-chip experiments.

Scientific Applications:

• Transcription factor binding analysis: Analyzes transcription factor binding in ChIP-chip datasets using the Joint Binding Deconvolution algorithm.
• Gene expression analysis: Integrates gene expression data with genomic and functional annotations for expression studies.
• Comparative genomics: Enables cross-species and multiple genome-build comparative analyses.
• Hypothesis-driven investigation: Supports formulation and recording of binding hypotheses to relate and compare ChIP-chip experiments.

Methodology:

GSE represents biological data streams via the GSEBricks middle software layer, uses a Java-based visualizer that communicates over a network with the database, performs storage, retrieval, and analysis of high-throughput microarray datasets, and applies a published Joint Binding Deconvolution algorithm to ChIP-chip data.