FFGED

FFGED curates and enables analysis of gene expression data from filamentous fungi to support functional genomics, transcriptional profiling, and comparative regulatory network studies.

Key Features:

• Data organization and submission: Structured storage of experimental metadata, experimental design, raw data, normalized details, and analysis results for gene expression experiments.
• Active experiment database: Support for submission and accumulation of multiple experiments over the course of research to enable progressive data aggregation and sharing.
• Cross-experiment linking: Association of related experiments to correlate gene expression levels across different experimental designs and conditions.
• Data management and analysis tools: Integrated tools for data submission, sharing, retrieval, and visualization of gene expression datasets.

Scientific Applications:

• Functional genomics and annotation: Aggregation of expression data and community-provided annotation and phenotypic information to support gene function assignment.
• Transcriptional profiling: Analysis of temporal and condition-dependent expression changes, including studies such as conidial germination in Neurospora crassa, to enable functional predictions of genes.
• Regulatory network characterization: Identification and characterization of transcriptional regulatory networks and comparison of network features across species to study evolution and niche adaptation.
• Comparative genomics: Comparative analysis of expression and interaction networks among closely and distantly related species to assess conservation and divergence of gene interactions.

Methodology:

Supported experimental and analytical methods include oligonucleotide-based microarrays for expression measurement; Bayesian analysis for estimating relative expression changes over time; hierarchical clustering and functional classification database use for grouping and characterizing expression patterns; and consensus motif searches to identify regulatory components.