P-POD The Princeton Protein Orthology Database Literature Discussion Tim Hulsen

6/3/2015 |P-POD |2 P-POD - Manuscript The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists Heinicke S 1,*, Livstone MS 1,*, Lu C 1,*, Oughtred R 1,*, Kang F 1, Angiuoli SV 2,3, White O 2, Botstein D 1, Dolinski K 1 PLoS ONE Aug 22; 2(1): e766 PubMed ID Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America. 2 The Institute for Genomic Research, Rockville, Maryland, United States of America 3 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America * These authors contributed equally to this work

6/3/2015 |P-POD |3 P-POD - Introduction Existing: many biological databases that provide comparative genomics information and tools None of these combine results from multiple comparative genomics methods with manually curated information from the literature  P-POD: Princeton Protein Orthology Database: –Visualizes phylogenetic relationships among predicted orthologs –Shows the orthologs in a wider evolutionary context –Contains experimental results manually collected from the literature, that can be compared to the computational analyses –Shows links to relevant human disease and gene information via the OMIM, model organism and sequence database

6/3/2015 |P-POD |4 P-POD – Ortholog methods Orthology is determined using OrthoMCL: –Can be run on multiple species at once –One of the better performing algorithms in terms of sensitivity and specificity (Alexeyenko et al., 2006 and Chen et al., 2007) Evolutionary context is determined using Jaccard: –Clustering algorithm to find related proteins –Larger groups than just orthologs –Manuscript in preparation

6/3/2015 |P-POD |5 P-POD – Covered species P-POD contains 8 species: Plasmodium falciparum Homo sapiens Drosophila melanogaster Mus musculus Arabidopsis thaliana Caenorhabditis elegans Danio rerio Saccharomyces cerevisiae  Most widely studied organisms, from a wide evolutionary range

6/3/2015 |P-POD |6 P-POD – Source Species Databases

6/3/2015 |P-POD |7 P-POD – Supported identifiers Organism Source Database Valid gene/protein identifier(s)Examples P.falciparumPlasmoDBPlasmoDB IDPF08_0034 H.sapiensENSEMBLENSEMBL peptide ID, peptide nameENSP ENSP , CDK2CDK2 D.melanogasterFlyBaseFlyBase IDCG17520-PACG17520-PA, CkIIalpha-PACkIIalpha-PA M.musculusENSEMBLENSEMBL peptide IDENSMUSP A.thalianaTAIRTAIR identifier or gene nameAT1G AT1G , PAB4PAB4 C.elegansWormBaseWormBase identifier or gene nameC09G4.1C09G4.1, dbr-1dbr-1 D.rerioENSEMBLENSEMBL peptide ID, ZFIN ID ENSDARP ENSDARP , ZDB-GENE ZDB-GENE S.cerevisiaeSGDORF name or gene nameYNL098CYNL098C, DPM1DPM1 + OMIM IDs

6/3/2015 |P-POD |8 P-POD – Orthology and clustering numbers 25,271 OrthoMCL families 15,050 Jaccard Clustering families 165,970 proteins (154,736 OrthoMCL and 152,799 Jaccard) 984 families containing proteins in all species (‘omnipresent’) 112 families with exactly one protein in each of the 8 species: involved in core biological processes, such as: –Translation –Transport –Cell cycle regulation –Cytoskeleton organization

6/3/2015 |P-POD |9 P-POD – Proteins in families, and orphans Relatively low percentages of orphans (<=13%, except for S. cerevisiae and P. falciparum) These numbers confirm the high conservation of proteins across eukaryotes, with the notable exception the Plasmodium outlier Yeast: complete protein set used, including 800 ORFS flagged as “Dubious” by SGD. If these are excluded, the percentage of orphans drops to 20%

6/3/2015 |P-POD |10 P-POD – Compared to other orthology databases Tot.

6/3/2015 |P-POD |11 P-POD - Pipeline

6/3/2015 |P-POD |12 P-POD – Pipeline Components [4] Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178–2189 [5] Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680 [29] Samuel Lattimore B, van Dongen S, Crabbe MJ (2005) GeneMCL in microarray analysis. Comput Biol Chem 29: 354– 359

6/3/2015 |P-POD |13 P-POD – The Database P-POD uses the Generic Model Organism Database (GMOD) database package using PostgreSQL software GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at many large and small community databases Other popular GMOD tools are Apollo (Genome annotation editor), Gbrowse (Genome annotation viewer), Cmap (Comparative map viewer), Sybil (Comparative genome viewer), Chado (Biological database schema) and BioMart (Data mining system)

6/3/2015 |P-POD |14 P-POD - Web Interface (1) The web interface allows users to search and browse the data in several ways Results can be queried by various peptide identifiers or gene names Searches generate result pages that contain: –a hyperlinked phylogenetic tree of predicted orthologs generated by OrthoMCL or of more distantly-related proteins generated by Jaccard clustering –a list of diseases and genes associated with the human ortholog(s) as documented in OMIM –a manually curated list of papers with cross-complementation experiments involving the yeast ortholog(s), from SGD database –a downloadable ClustalW alignment of family members Web address:

6/3/2015 |P-POD |15 P-POD – Web Interface (2) OrthoMCL OMIM CLUSTALW SGD Lit. INPUT

6/3/2015 |P-POD |16 P-POD – Web Interface (3) SGD Lit. CLUSTALW JACCARD

6/3/2015 |P-POD |17 P-POD – Comparison of methods Orthology/clustering methods OrthoMCL and Jaccard can be compared using P-POD Jaccard is far more inclusive than OrthoMCL Shown at the right: OrthoMCL family of the alpha tubulins. It contains only the alpha tubulins, while the Jaccard family contains the alpha, beta, and gamma tubulins

6/3/2015 |P-POD |18 P-POD – Discussion (1) P-POD shows direct orthology (OrthoMCL) and broader evolutionary clustering (Jaccard) P-POD uses a generic, modular database schema (GMOD) in combination with a freely available database system (PostgreSQL) P-POD provides experimental evidence of conservation curated from the primary literature Three sets of users: –Molecular biologists that query the database over the web to browse orthology data for their favorite proteins –Model organism database developers, who will quickly be able to provide comparative genomics tools with their species of interest by implementing our system –Computational biologists who are developing novel comparative genomics algorithms will find the curated information and computational data from other methods extremely useful in assessing their approach

6/3/2015 |P-POD |19 P-POD – Discussion (2) P-POD can be downloaded in its entirety for installation on one’s own system Software developers can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools

6/3/2015 |P-POD |20 P-POD – Future plans Provide regular updates to the data contained within the database Add new features to the web interface Expand upon the amount of data stored within the database Provide curated literature describing experimental confirmation of orthology Include literature from other species than just S. cerevisiae As more refined methods for automatic detection of orthology are developed, they can be incorporated into the P-POD tool, taking advantage of the modular design scheme