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Open Access Methodology article

Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution

Marie C Galligan12*, Radka Saldova2, Matthew P Campbell3, Pauline M Rudd2 and Thomas B Murphy1

Author Affiliations

1 School of Mathematical Sciences, University College Dublin, Belfield, Dublin 4, Ireland

2 NIBRT Dublin Oxford Glycobiology Laboratory, NIBRT, Mount Merrion, Blackrock, Dublin 4, Ireland

3 Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, New South Wales 2109, Australia

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BMC Bioinformatics 2013, 14:155  doi:10.1186/1471-2105-14-155

Published: 7 May 2013

Abstract

Background

Glycoproteins are involved in a diverse range of biochemical and biological processes. Changes in protein glycosylation are believed to occur in many diseases, particularly during cancer initiation and progression. The identification of biomarkers for human disease states is becoming increasingly important, as early detection is key to improving survival and recovery rates. To this end, the serum glycome has been proposed as a potential source of biomarkers for different types of cancers.

High-throughput hydrophilic interaction liquid chromatography (HILIC) technology for glycan analysis allows for the detailed quantification of the glycan content in human serum. However, the experimental data from this analysis is compositional by nature. Compositional data are subject to a constant-sum constraint, which restricts the sample space to a simplex. Statistical analysis of glycan chromatography datasets should account for their unusual mathematical properties.

As the volume of glycan HILIC data being produced increases, there is a considerable need for a framework to support appropriate statistical analysis. Proposed here is a methodology for feature selection in compositional data. The principal objective is to provide a template for the analysis of glycan chromatography data that may be used to identify potential glycan biomarkers.

Results

A greedy search algorithm, based on the generalized Dirichlet distribution, is carried out over the feature space to search for the set of “grouping variables” that best discriminate between known group structures in the data, modelling the compositional variables using beta distributions. The algorithm is applied to two glycan chromatography datasets. Statistical classification methods are used to test the ability of the selected features to differentiate between known groups in the data. Two well-known methods are used for comparison: correlation-based feature selection (CFS) and recursive partitioning (rpart). CFS is a feature selection method, while recursive partitioning is a learning tree algorithm that has been used for feature selection in the past.

Conclusions

The proposed feature selection method performs well for both glycan chromatography datasets. It is computationally slower, but results in a lower misclassification rate and a higher sensitivity rate than both correlation-based feature selection and the classification tree method.

Keywords:
Compositional data; Beta distribution; Generalized Dirichlet distribution; Variable selection; Feature selection; Correlation-based feature selection; Recursive partitioning; Glycobiology; Glycan; HILIC; Chromatography data