CDH

CDH identifies co-regulated genes in Tetrahymena thermophila using transcriptomic data to predict gene function and infer pathway-specific machinery.

Key Features:

• Gene-centric query: Starts from a gene of interest to identify co-regulated counterparts.
• Transcriptome integration: Accesses the Tetrahymena transcriptome database to detect co-regulation relationships.
• Ortholog detection: Performs reciprocal BLAST searches to identify orthologs in other organisms.
• Annotation aggregation: Collates annotations of identified orthologs to support functional inference.
• Pathway component identification: Uses co-regulation patterns to define pathway-specific machinery within the organism.
• Cross-species inference: Leverages conserved ortholog information to broaden functional inference beyond Tetrahymena thermophila.
• Automated analysis: Automates identification of co-regulated genes and collation of ortholog annotations.

Scientific Applications:

• Gene function prediction: Infers putative functions of genes in Tetrahymena thermophila based on co-regulation and ortholog annotations.
• Pathway analysis: Identifies pathway-specific machinery and aids reconstruction of cellular pathways from co-regulated gene sets.
• Comparative genomics: Enables functional inference in other organisms by leveraging conserved ortholog annotations identified via BLAST.
• Genome annotation support: Assists annotation of sparsely annotated genomes by transferring functional information from orthologs.

Methodology:

Starts from a gene of interest, queries the Tetrahymena transcriptome database to identify co-regulated genes, performs reciprocal BLAST searches to find orthologs in other organisms, and collates ortholog annotations to infer gene function.