ProteinHistorian

ProteinHistorian estimates phylogenetic ages of proteins and analyzes their evolutionary history to provide insights into functional evolution and cellular roles.

Key Features:

• Phylogenetic Age Estimation: Estimates evolutionary ages of proteins from user-provided protein lists using multiple algorithms and diverse databases of evolutionary relationships, allowing alternative definitions of protein age.
• Enrichment Analysis: Quantifies enrichment for proteins of specific phylogenetic ages within sets of interest to identify non-random age distributions.
• Comparative Functional Insights: Reveals correlations between protein age and attributes such as expression levels, regulatory functions, and catalytic activities, including observations that proteins highly expressed in humans compared to chimpanzees and rhesus macaques tend to be younger while regulatory proteins are generally more recent than catalytic proteins.
• Cross-Species Analysis: Supports comparative analyses across over thirty eukaryotic species and includes pre-computed ages for 32 eukaryotic genomes.
• Integration with Other Attributes: Enables combination of age analysis with additional user-supplied protein attributes for multifactor investigations.
• Modular and Extensible Design: Employs an architecture intended to facilitate incorporation of new datasets and algorithms as they become available.

Scientific Applications:

• Evolutionary Biology: Infers the timing of protein origin and patterns of gain and loss across lineages to study evolutionary trajectories.
• Functional Genomics: Links protein age to functional annotations and expression patterns to interpret genomic and transcriptomic variation.
• Proteomics: Interprets proteome composition and age-related functional shifts relevant to cellular roles and adaptations.
• Disease and Developmental Studies: Supports hypothesis generation about how protein age relates to disease mechanisms, developmental stages, and species-specific adaptations.

Methodology:

Estimates protein phylogenetic ages using multiple algorithms and databases of evolutionary relationships from user-provided protein lists, performs statistical enrichment analyses of age distributions, integrates additional protein attributes, and utilizes pre-computed ages for 32 eukaryotic genomes.