HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms

Maria Persico,Caius Gavrila,Arnaud Ceol,Gianni Cesareni,Arnaldo Florio,Robert Hoffmann

doi:10.1186/1471-2105-6-s4-s21

Maria Persico, Caius Gavrila + Show 4 more

Open Access

https://doi.org/10.1186/1471-2105-6-s4-s21

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Abstract

BackgroundThe application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such genome-wide approaches have not been applied to the human proteome.ResultsIn order to fill this gap we have assembled an inferred human protein interaction network where interactions discovered in model organisms are mapped onto the corresponding human orthologs. In addition to a stringent assignment to orthology classes based on the InParanoid algorithm, we have implemented a string matching algorithm to filter out orthology assignments of proteins whose global domain organization is not conserved. Finally, we have assessed the accuracy of our own, and related, inferred networks by benchmarking them against i) an assembled experimental interactome, ii) a network derived by mining of the scientific literature and iii) by measuring the enrichment of interacting protein pairs sharing common Gene Ontology annotation.ConclusionThe resulting networks are named HomoMINT and HomoMINT_filtered, the latter being based on the orthology table filtered by the domain architecture matching algorithm. They contains 9749 and 5203 interactions respectively and can be analyzed and viewed in the context of the experimentally verified interactions between human proteins stored in the MINT database. HomoMINT is constantly updated to take into account the growing information in the MINT database.

Highlights

The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms
High throughput approaches based on the yeast two hybrid [1] and TAP TAG [2] methods have provided for the first time a genome-wide perspective of the interactome of simple model organisms such as H. pylori[3], E. coli[4], S. cerevisiae [5,6,7,8], C. elegans [9] and D. melanogaster[10,11]
HomoMINT Our strategy starts by assigning proteins to orthology groups having a human protein as the main ortholog

Summary

Introduction

The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, such genome-wide approaches have not been applied to the human proteome. Edges marked by small blue circles indicate that the corresponding interactions were inferred from experiments carried out in model organisms, while yellow circles mark interactions supported by direct experimental results. Interactions that are inferred from model organisms but are supported by direct experiments are marked by yellow circles with a blue contour. A series of check boxes make it possible to visualize interactions inferred by any combination of model organism interactomes

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Discussion

Conclusion