Interolog Regulog Database

Interolog Regulog Database maps conserved protein–protein and protein–DNA interactions and conserved regulatory relationships (interologs and regulogs) across species to support comparative genomics and the prediction of conserved interactions.

Key Features:

• Interolog Mapping: Quantitatively assesses transferability of protein–protein interactions between species by computing joint sequence identity and joint E-values using the geometric means of pairwise metrics and applying thresholds of >80% joint identity or joint E-value < 1e-70.
• Protein–DNA Interaction Conservation: Identifies conserved protein–DNA binding interactions across species using family-specific sequence identity thresholds ranging from 30% to 60%.
• Regulog Concept: Maps regulogs as conserved regulatory relationships between proteins across species to infer preserved regulatory mechanisms.
• Cross-Species Application: Transfers interologs and regulogs from model organisms such as Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori to less-annotated genomes such as Arabidopsis thaliana, producing predictions including approximately 90,000 potential protein–protein interactions in C. elegans.
• Statistical Validation: Reports that a subset of predicted interactions were validated by two-hybrid experiments and that 45 transferred C. elegans interactions were experimentally verified and found to be statistically significant.

Scientific Applications:

• Evolutionary Biology: Enables study of conservation and divergence of protein interactions and regulatory relationships across species.
• Functional Genomics: Supports prediction of protein function and interaction networks in less-characterized genomes by transferring annotations from model organisms.
• Systems Biology: Facilitates construction and comparison of cross-species interaction networks for systems-level analyses.
• Experimental Design and Hypothesis Generation: Provides ranked predictions to guide experimental validation such as two-hybrid assays and targeted studies of conserved regulation.

Methodology:

Performs interolog mapping via comparative genomics, computes geometric means of pairwise sequence identities and E-values for interacting protein pairs, and applies explicit thresholds (>80% joint identity or joint E-value < 1e-70) and family-specific 30–60% identity cutoffs for protein–DNA conservation.