Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder

Genomic psychiatry is a recently expanding field which holds much promise in biomarker discovery for psychiatric disorders. However, high dimensionality of genomic data and relative smaller cohort sizes at the psychiatric outpatient clinic imposes a significant challenge for clinically significant a...

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Main Author: Zeng, Yanxi
Other Authors: Jagath C Rajapakse
Format: Final Year Project
Language:English
Published: Nanyang Technological University 2021
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Online Access:https://hdl.handle.net/10356/149051
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-1490512021-05-25T02:23:21Z Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder Zeng, Yanxi Jagath C Rajapakse School of Computer Science and Engineering ASJagath@ntu.edu.sg Engineering::Computer science and engineering Genomic psychiatry is a recently expanding field which holds much promise in biomarker discovery for psychiatric disorders. However, high dimensionality of genomic data and relative smaller cohort sizes at the psychiatric outpatient clinic imposes a significant challenge for clinically significant analysis of transcriptomic data. We approach this problem using state-of- the-art machine-learning methods to extract the salient features of genomic data for potential use as biomarkers. To simulate application to psychiatric outpatient clinics, we investigate the use of the above methods on transcriptomic data of lithium treated bipolar patients (n=240) and healthy controls (n=240). After a gamut of preliminary univariate feature selection methods, we apply multivariate methods such as the recursive feature elimination with various machine learning models on transcriptomic data with nested cross-validation to select the set of genes giving the best predictive accuracy of diagnosis. Our results indicated that the genes selected with the above-mentioned process achieve higher predictive classification accuracies of the clinical outcomes and the use of lithium treatment. Furthermore, gene set enrichment analysis and gene ontology analysis were carried out on the candidate biomarkers for investigation of underlying biological and pathogenic processes. We conclude that a feature selection pipeline combining univariate filtering and machine learning based feature selection methods is capable of overcoming the challenges of high dimensionality in genomic data and extracting salient features highlighting related biological pathways for downstream analysis. Bachelor of Engineering (Computer Science) 2021-05-25T02:23:21Z 2021-05-25T02:23:21Z 2021 Final Year Project (FYP) Zeng, Y. (2021). Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/149051 https://hdl.handle.net/10356/149051 en SCSE20-0258 application/pdf Nanyang Technological University
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Computer science and engineering
spellingShingle Engineering::Computer science and engineering
Zeng, Yanxi
Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
description Genomic psychiatry is a recently expanding field which holds much promise in biomarker discovery for psychiatric disorders. However, high dimensionality of genomic data and relative smaller cohort sizes at the psychiatric outpatient clinic imposes a significant challenge for clinically significant analysis of transcriptomic data. We approach this problem using state-of- the-art machine-learning methods to extract the salient features of genomic data for potential use as biomarkers. To simulate application to psychiatric outpatient clinics, we investigate the use of the above methods on transcriptomic data of lithium treated bipolar patients (n=240) and healthy controls (n=240). After a gamut of preliminary univariate feature selection methods, we apply multivariate methods such as the recursive feature elimination with various machine learning models on transcriptomic data with nested cross-validation to select the set of genes giving the best predictive accuracy of diagnosis. Our results indicated that the genes selected with the above-mentioned process achieve higher predictive classification accuracies of the clinical outcomes and the use of lithium treatment. Furthermore, gene set enrichment analysis and gene ontology analysis were carried out on the candidate biomarkers for investigation of underlying biological and pathogenic processes. We conclude that a feature selection pipeline combining univariate filtering and machine learning based feature selection methods is capable of overcoming the challenges of high dimensionality in genomic data and extracting salient features highlighting related biological pathways for downstream analysis.
author2 Jagath C Rajapakse
author_facet Jagath C Rajapakse
Zeng, Yanxi
format Final Year Project
author Zeng, Yanxi
author_sort Zeng, Yanxi
title Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
title_short Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
title_full Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
title_fullStr Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
title_full_unstemmed Feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
title_sort feature selection on transcriptome data for identification of novel biomarkers for bipolar disorder
publisher Nanyang Technological University
publishDate 2021
url https://hdl.handle.net/10356/149051
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