Cancer module genes ranking using kernelized score functions

Matteo Re,Giorgio Valentini

doi:10.1186/1471-2105-13-s14-s3

Abstract

BackgroundCo-expression based Cancer Modules (CMs) are sets of genes that act in concert to carry out specific functions in different cancer types, and are constructed by exploiting gene expression profiles related to specific clinical conditions or expression signatures associated to specific processes altered in cancer. Unfortunately, genes involved in cancer are not always detectable using only expression signatures or co-expressed sets of genes, and in principle other types of functional interactions should be exploited to obtain a comprehensive picture of the molecular mechanisms underlying the onset and progression of cancer.ResultsWe propose a novel semi-supervised method to rank genes with respect to CMs using networks constructed from different sources of functional information, not limited to gene expression data. It exploits on the one hand local learning strategies through score functions that extend the guilt-by-association approach, and on the other hand global learning strategies through graph kernels embedded in the score functions, able to take into account the overall topology of the network. The proposed kernelized score functions compare favorably with other state-of-the-art semi-supervised machine learning methods for gene ranking in biological networks and scales well with the number of genes, thus allowing fast processing of very large gene networks.ConclusionsThe modular nature of kernelized score functions provides an algorithmic scheme from which different gene ranking algorithms can be derived, and the results show that using integrated functional networks we can successfully predict CMs defined mainly through expression signatures obtained from gene expression data profiling. A preliminary analysis of top ranked "false positive" genes shows that our approach could be in perspective applied to discover novel genes involved in the onset and progression of tumors related to specific CMs.

Highlights

Co-expression based Cancer Modules (CMs) are sets of genes that act in concert to carry out specific functions in different cancer types, and are constructed by exploiting gene expression profiles related to specific clinical conditions or expression signatures associated to specific processes altered in cancer
Methods at first we describe the Cancer gene Modules (CMs) proposed in [9] and the functional interaction networks used in our experiments to rank genes according to their likelihood to belong to specific CMs
[14] Wu and colleagues constructed a functional protein interaction network (FI) based on functional interactions predicted by a Naive Bayes classifier (NBC) trained on pairwise relationships extracted from Reactome [21] and other curated pathways databases, and from uncurated pairwise relationships derived from physical protein-protein interactions (PPI) in human and other species, from gene co-expression data, proteins domain-domain interactions, protein interactions obtained via biomedical text mining, and Gene Ontology annotations

Summary

Introduction

Co-expression based Cancer Modules (CMs) are sets of genes that act in concert to carry out specific functions in different cancer types, and are constructed by exploiting gene expression profiles related to specific clinical conditions or expression signatures associated to specific processes altered in cancer. Even if novel bio-technologies, such as Generation Sequencing and epigenetic pattern analysis, have been recently applied to cancer research [4], a fundamental contribution in this research area is still due to the application of gene expression profiling. This technique proved to be effective for the classification of diverse types of tumors [5], for the prediction of patients outcome [6] and the prediction of the response to chemotherapies [7,8]

Methods

Results

Conclusion