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

Hdl Handle:
http://hdl.handle.net/10147/295444
Title:
Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution
Authors:
Galligan, Marie C; Saldova, Radka; Campbell, Matthew P; Rudd, Pauline M; Murphy, Thomas B
Citation:
BMC Bioinformatics. 2013 May 07;14(1):155
Issue Date:
7-May-2013
URI:
http://dx.doi.org/10.1186/1471-2105-14-155; http://hdl.handle.net/10147/295444
Abstract:
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.
Item Type:
Journal Article

Full metadata record

DC FieldValue Language
dc.contributor.authorGalligan, Marie C-
dc.contributor.authorSaldova, Radka-
dc.contributor.authorCampbell, Matthew P-
dc.contributor.authorRudd, Pauline M-
dc.contributor.authorMurphy, Thomas B-
dc.date.accessioned2013-07-08T08:43:58Z-
dc.date.available2013-07-08T08:43:58Z-
dc.date.issued2013-05-07-
dc.identifier.citationBMC Bioinformatics. 2013 May 07;14(1):155-
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-14-155-
dc.identifier.urihttp://hdl.handle.net/10147/295444-
dc.description.abstractAbstract 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.-
dc.titleGreedy feature selection for glycan chromatography data with the generalized Dirichlet distribution-
dc.typeJournal Article-
dc.language.rfc3066en-
dc.rights.holderMarie C Galligan et al.; licensee BioMed Central Ltd.-
dc.description.statusPeer Reviewed-
dc.date.updated2013-07-06T15:09:40Z-
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