The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists
Author Information
Author(s): Heinicke Sven, Livstone Michael S., Lu Charles, Oughtred Rose, Kang Fan, Angiuoli Samuel V., White Owen, Botstein David, Dolinski Kara
Primary Institution: Princeton University
Hypothesis
To create a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs to a query gene from various eukaryotic organisms.
Conclusion
P-POD provides a comprehensive comparative genomics analysis system that integrates computational analyses with manually curated literature.
Supporting Evidence
- P-POD integrates results from multiple comparative genomics methods with curated literature.
- The database includes protein sequences from eight eukaryotic organisms chosen for their medical value or status as model organisms.
- P-POD allows users to visualize phylogenetic relationships among predicted orthologs.
- The system is designed to be user-friendly for experimental biologists.
- P-POD provides links to relevant human disease and gene information.
Takeaway
P-POD is a tool that helps scientists see how genes from different organisms are related and understand their evolutionary history.
Methodology
The P-POD pipeline uses OrthoMCL and Jaccard clustering to analyze protein sequences and visualize phylogenetic relationships.
Potential Biases
Potential biases may arise from the reliance on computational predictions for ortholog identification.
Limitations
The database may include extraneous paralogs due to the selection of species and the limitations of computational methods.
Statistical Information
P-Value
p<0.05
Digital Object Identifier (DOI)
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