DGD

DGD identifies and catalogs groups of duplicated genes across nine species to enable analysis of their genomic co-location, co-expression, and functional similarity.

Key Features:

• Species coverage: Analyses are provided for nine different species.
• Duplication identification: Pairwise BLAST (Basic Local Alignment Search Tool) comparisons on peptide sequences of genes mapped on the same chromosome combined with genomic location information define groups of duplicated genes.
• Co-expression analysis: Pearson correlations are computed between gene expression profiles for genes within each duplicated group when expression data are available.
• Functional similarity: Semantic similarities among functional Gene Ontology (GO) annotations are computed for genes within groups when GO annotations are available.
• Output data: Lists of co-located duplicated genes annotated with co-expression values and semantic similarity scores.

Scientific Applications:

• Genome structure–function analysis: Investigate relationships between genomic co-location of duplicated genes and their expression or functional similarity.
• Evolutionary dynamics of gene duplication: Compare divergence in expression and functional annotation among duplicated genes.
• Gene expression studies: Assess co-expression patterns among duplicated genes across available expression datasets.

Methodology:

Pairwise BLAST (Basic Local Alignment Search Tool) on peptide sequences of genes mapped to the same chromosome to define duplicated gene groups; computation of Pearson correlations between gene expression data; computation of semantic similarities among Gene Ontology (GO) functional annotations.