Principal component analysis based unsupervised feature extraction applied to bioinformatics analysis

2017 ◽  
pp. 153-182 ◽  
Author(s):  
Y-h. Taguchi ◽  
Mitsuo Iwadate ◽  
Hideaki Umeyama ◽  
Yoshiki Murakami
Keyword(s):  
Principal Component Analysis ◽  
Feature Extraction ◽  
Bioinformatics Analysis ◽  
Principal Component ◽  
Component Analysis ◽  
Unsupervised Feature Extraction

scholarly journals Effects of Collagen–Glycosaminoglycan Mesh on Gene Expression as Determined by Using Principal Component Analysis-Based Unsupervised Feature Extraction

Polymers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 4117
Author(s):  
Y-h. Taguchi ◽  
Turki Turki
Keyword(s):  
Gene Expression ◽  
Principal Component Analysis ◽  
Feature Extraction ◽  
Cell Lines ◽  
Time Course ◽  
Expression Profiles ◽  
Principal Component ◽  
Component Analysis ◽  
Altered Expression ◽  
Unsupervised Feature Extraction

The development of the medical applications for substances or materials that contact cells is important. Hence, it is necessary to elucidate how substances that surround cells affect gene expression during incubation. In the current study, we compared the gene expression profiles of cell lines that were in contact with collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

Heuristic Principal Component Analysis-Based Unsupervised Feature Extraction and Its Application to Bioinformatics

2015 ◽  
pp. 138-162 ◽  
Author(s):  
Y-H. Taguchi ◽  
Mitsuo Iwadate ◽  
Hideaki Umeyama ◽  
Yoshiki Murakami ◽  
Akira Okamoto
Keyword(s):  
Principal Component Analysis ◽  
Feature Extraction ◽  
Principal Component ◽  
Component Analysis ◽  
Circulating Microrna ◽  
Biomarker Identification ◽  
Typical Situation ◽  
Aberrant Dna Methylation ◽  
The Stability ◽  
Unsupervised Feature Extraction

Feature Extraction (FE) is a difficult task when the number of features is much larger than the number of samples, although that is a typical situation when biological (big) data is analyzed. This is especially true when FE is stable, independent of the samples considered (stable FE), and is often required. However, the stability of FE has not been considered seriously. In this chapter, the authors demonstrate that Principal Component Analysis (PCA)-based unsupervised FE functions as stable FE. Three bioinformatics applications of PCA-based unsupervised FE—detection of aberrant DNA methylation associated with diseases, biomarker identification using circulating microRNA, and proteomic analysis of bacterial culturing processes—are discussed.

scholarly journals Effects of the collagen–glycosaminoglycan mesh on gene expression as determined by using principal component analysis-based unsupervised feature extraction

2021 ◽  
Author(s):  
Y-h. Taguchi ◽  
Turki Turki
Keyword(s):  
Gene Expression ◽  
Principal Component Analysis ◽  
Feature Extraction ◽  
Cell Lines ◽  
Time Course ◽  
Expression Profiles ◽  
Principal Component ◽  
Component Analysis ◽  
Altered Expression ◽  
Unsupervised Feature Extraction

AbstractDevelopment of the medical applications for substances or materials that contact the cells is important. Hence, it is necessary to elucidate how substance that surround cells affect the gene expression during incubation. Here, we compared the gene expression profiles of cell lines that were in contact with the collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

scholarly journals microRNA-mRNA interaction identification in Wilms tumor using principal component analysis based unsupervised feature extraction

2016 ◽  
Author(s):  
Y-h. Taguchi
Keyword(s):  
Principal Component Analysis ◽  
Feature Extraction ◽  
Wilms Tumor ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Correlation Coefficients ◽  
Principal Component ◽  
Component Analysis ◽  
Mrna Gene ◽  
Unsupervised Feature Extraction

AbstractWilms tumor is one of lethal child renal cancers, for which no known disease causing mechanisms exist. In this paper, we tried to identify possible disease causing microRNA(miRNA)-mRNA pairs (interactions) by analyzing (partially matched) miRNA/mRNA gene expression profiles with the recently proposed principal component analysis based unsupervised feature extraction. It successfully identified multiple miRNA-mRNA pairs whose biological natures are convincing. Correlation coefficients between miRNA and mRNA expression in matched parts of profiles turned out to be significantly negative. Constructed miRNA-mRNA network will be a key to understand Wilms tumor causing mechanisms.

scholarly journals Principal component analysis-based unsupervised feature extraction applied to single-cell gene expression analysis1

2018 ◽  
Author(s):  
Y-h. Taguchi
Keyword(s):  
Principal Component Analysis ◽  
Feature Extraction ◽  
Single Cell ◽  
Expression Profiles ◽  
Principal Component ◽  
Component Analysis ◽  
Experimental Conditions ◽  
Biologically Relevant ◽  
Cell Gene Expression ◽  
Unsupervised Feature Extraction

AbstractDue to missed sample labeling, unsupervised feature selection during single-cell (sc) RNA-seq can identify critical genes under the experimental conditions considered. In this paper, we applied principal component analysis (PCA)-based unsupervised feature extraction (FE) to identify biologically relevant genes from mouse and human embryonic brain development expression profiles retrieved by scRNA-seq. When evaluating the biological relevance of selected genes by various enrichment analyses, the PCA-based unsupervised FE outperformed conventional unsupervised approaches that select highly variable genes as well as bimodal genes in addition to the recently proposed dpFeature.

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