Protein function prediction from protein-protein interaction network using gene ontology based neighborhood analysis and physico-chemical features.

Abstract

Protein Function Prediction from Protein-Protein Interaction Network (PPIN) and physico-chemical features using the Gene Ontology (GO) classification are indeed very useful for assigning biological or biochemical functions to a protein. They also lead to the identification of those significant proteins which are responsible for the generation of various diseases whose drugs are still yet to be discovered. So, the prediction of GO functional terms from PPIN and sequence is an important field of study. In this work, we have proposed a methodology, Multi Label Protein Function Prediction (ML_PFP) which is based on Neighborhood analysis empowered with physico-chemical features of constituent amino acids to predict the functional group of unannotated protein. A protein does not perform functions in isolation rather it performs functions in a group by interacting with others. So a protein is involved in many functions or, in other words, may be associated with multiple functional groups or labels or GO terms. Though functional group of other known interacting partner protein and its physico-chemical features provide useful information, assignment of multiple labels to unannotated protein is a very challenging task. Here, we have taken Homo sapiens or Human PPIN as well as Saccharomyces cerevisiae or yeast PPIN along with their GO terms to predict functional groups or GO terms of unannotated proteins. This work has become very challenging as both Human and Yeast protein dataset are voluminous and complex in nature and multi-label functional groups assignment has also added a new dimension to this challenge. Our algorithm has been observed to achieve a better performance in Cellular Function, Molecular Function and Biological Process of both yeast and human network when compared with the other existing state-of-the-art methodologies which will be discussed in detail in the results section.