Interolog Regulog Database

Interolog Regulog Database maps conserved protein-protein and protein-DNA interactions across species via interolog mapping and regulog identification to enable functional annotation transfer and comparative analysis.

Key Features:

• Interolog Mapping: Transfers protein-protein interaction annotations between species using joint sequence identity and joint E-values with reliable transfers observed at joint sequence identity >80% or joint E-value < 1e-70.
• Protein-DNA Interaction Analysis: Extends interolog analysis to protein-DNA binding interactions conserved across species with sequence-identity thresholds ranging from 30% to 60% depending on the protein family.
• Regulog Identification: Identifies and maps conserved regulatory relationships (regulogs) between proteins across species to capture conserved regulatory network relationships beyond direct physical interactions.
• Cross-Species Mapping: Maps interologs and regulogs from Saccharomyces cerevisiae to other genomes, including Arabidopsis thaliana, and transferred approximately 90,000 potential protein-protein interactions to Caenorhabditis elegans.
• Experimental Validation: A subset of predicted interologs was tested with two-hybrid experiments, yielding 45 verified overlaps that were statistically significant.

Scientific Applications:

• Interaction Prediction: Predicts protein-protein and protein-DNA interactions in organisms with limited experimental annotations by transferring evidence from model organisms.
• Evolutionary Conservation Analysis: Assesses conservation of functional interactions and regulatory relationships across species.
• Discovery of Novel Interactions and Pathways: Facilitates identification of novel interaction partners and pathways by leveraging known interactions from well-characterized model organisms.

Methodology:

Quantitative assessment of sequence similarity using joint sequence identity and joint E-values, computation of geometric means for joint sequence identities or E-values, and application of explicit thresholds (e.g., >80% joint identity or <1e-70 joint E-value for protein-protein interactions; 30–60% identity ranges for protein-DNA interactions) to determine reliable interolog and regulog transfers.