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Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Joint Authors
Dou, Yongchao
Guo, Xiaomei
Yuan, Lingling
Holding, David R.
Zhang, Chi
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-08-03
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
To improve the applicability of RNA-seq technology, a large number of RNA-seq data analysis methods and correction algorithms have been developed.
Although these new methods and algorithms have steadily improved transcriptome analysis, greater prediction accuracy is needed to better guide experimental designs with computational results.
In this study, a new tool for the identification of differentially expressed genes with RNA-seq data, named GExposer, was developed.
This tool introduces a local normalization algorithm to reduce the bias of nonrandomly positioned read depth.
The naive Bayes classifier is employed to integrate fold change, transcript length, and GC content to identify differentially expressed genes.
Results on several independent tests show that GExposer has better performance than other methods.
The combination of the local normalization algorithm and naive Bayes classifier with three attributes can achieve better results; both false positive rates and false negative rates are reduced.
However, only a small portion of genes is affected by the local normalization and GC content correction.
American Psychological Association (APA)
Dou, Yongchao& Guo, Xiaomei& Yuan, Lingling& Holding, David R.& Zhang, Chi. 2015. Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization. BioMed Research International،Vol. 2015, no. 2015, pp.1-9.
https://search.emarefa.net/detail/BIM-1056729
Modern Language Association (MLA)
Dou, Yongchao…[et al.]. Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization. BioMed Research International No. 2015 (2015), pp.1-9.
https://search.emarefa.net/detail/BIM-1056729
American Medical Association (AMA)
Dou, Yongchao& Guo, Xiaomei& Yuan, Lingling& Holding, David R.& Zhang, Chi. Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-9.
https://search.emarefa.net/detail/BIM-1056729
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1056729