Applications of Different Weighting Schemes to Improve Pathway-Based Analysis
Joint Authors
Ha, Sook S.
Xuan, Jianhua
Kim, Inyoung
Wang, Yue Joseph
Source
International Journal of Genomics
Issue
Vol. 2011, Issue 2011 (31 Dec. 2011), pp.1-15, 15 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2011-04-06
Country of Publication
Egypt
No. of Pages
15
Main Subjects
Abstract EN
Conventionally, 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.
American Psychological Association (APA)
Ha, Sook S.& Kim, Inyoung& Wang, Yue Joseph& Xuan, Jianhua. 2011. Applications of Different Weighting Schemes to Improve Pathway-Based Analysis. International Journal of Genomics،Vol. 2011, no. 2011, pp.1-15.
https://search.emarefa.net/detail/BIM-990483
Modern Language Association (MLA)
Ha, Sook S.…[et al.]. Applications of Different Weighting Schemes to Improve Pathway-Based Analysis. International Journal of Genomics No. 2011 (2011), pp.1-15.
https://search.emarefa.net/detail/BIM-990483
American Medical Association (AMA)
Ha, Sook S.& Kim, Inyoung& Wang, Yue Joseph& Xuan, Jianhua. Applications of Different Weighting Schemes to Improve Pathway-Based Analysis. International Journal of Genomics. 2011. Vol. 2011, no. 2011, pp.1-15.
https://search.emarefa.net/detail/BIM-990483
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-990483