Applications of Different Weighting Schemes to Improve Pathway-Based Analysis

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dc.contributor.authorHa, Sook S.en
dc.contributor.authorKim, Inyoungen
dc.contributor.authorWang, Yueen
dc.contributor.authorXuan, Jianhuaen
dc.contributor.departmentElectrical and Computer Engineeringen
dc.contributor.departmentStatisticsen
dc.date.accessioned2017-09-18T09:54:11Zen
dc.date.available2017-09-18T09:54:11Zen
dc.date.issued2011-05-22en
dc.date.updated2017-09-18T09:54:11Zen
dc.description.abstractConventionally, pathway-based analysis assumes that genes in a pathway equally contribute to a biological function, thus assigning uniform weight to genes. However, this assumption has been proved incorrect, and applying uniform weight in the pathway analysis may not be an appropriate approach for the tasks like molecular classification of diseases, as genes in a functional group may have different predicting power. Hence, we propose to use different weights to genes in pathway-based analysis and devise four weighting schemes. We applied them in two existing pathway analysis methods using both real and simulated gene expression data for pathways. Among all schemes, random weighting scheme, which generates random weights and selects optimal weights minimizing an objective function, performs best in terms of 𝑷 value or error rate reduction. Weighting changes pathway scoring and brings up some new significant pathways, leading to the detection of disease-related genes that are missed under uniform weight.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationSook S. Ha, Inyoung Kim, Yue Wang, and Jianhua Xuan, “Applications of Different Weighting Schemes to Improve Pathway-Based Analysis,” Comparative and Functional Genomics, vol. 2011, Article ID 463645, 15 pages, 2011. doi:10.1155/2011/463645en
dc.identifier.doihttps://doi.org/10.1155/2011/463645en
dc.identifier.urihttp://hdl.handle.net/10919/79029en
dc.language.isoenen
dc.publisherHindawien
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderCopyright © 2011 Sook S. Ha et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleApplications of Different Weighting Schemes to Improve Pathway-Based Analysisen
dc.title.serialComparative and Functional Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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