scholarly journals Tensor decomposition–based unsupervised feature extraction for integrated analysis of TCGA data on microRNA expression and promoter methylation of genes in ovarian cancer

2018 ◽  
Author(s):  
Y-h. Taguchi ◽  
Ka-Lok Ng
Keyword(s):  
Ovarian Cancer ◽  
Feature Extraction ◽  
Promoter Methylation ◽  
Ovarian Tissue ◽  
Tensor Decomposition ◽  
Biological Evaluation ◽  
Integrated Analysis ◽  
Tissue Samples ◽  
Expression Levels ◽  
Unsupervised Feature Extraction

AbstractIntegrated analysis of epigenetic profiles is important but difficult. Tensor decomposition–based unsupervised feature extraction was applied here to data on microRNA (miRNA) expression and promoter methylation of genes in ovarian cancer. It selected seven miRNAs and 241 genes by expression levels and promoter methylation degrees, respectively, such that they showed differences between eight normal ovarian tissue samples and 569 tumor samples. The expression levels of the seven miRNAs and the degrees of promoter methylation of the 241 genes also correlated significantly. Conventional Student’s t test–based feature selection failed to identify miRNAs and genes that have the above properties. On the other hand, biological evaluation of the seven identified miRNAs and 241 identified genes suggests that they are strongly related to cancer as expected.

scholarly journals Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method

2019 ◽  
Author(s):  
Ka-Lok Ng ◽  
Y-h Taguchi
Keyword(s):  
Feature Extraction ◽  
Cell Carcinoma ◽  
Complex Disease ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Expression Profiles ◽  
Tensor Decomposition ◽  
Renal Clear Cell Carcinoma ◽  
Integrated Analysis ◽  
Unsupervised Feature Extraction

AbstractCancer is a highly complex disease caused by multiple genetic factors. MicroRNA (miRNA) and mRNA expression profiles are useful for identifying prognostic biomarkers for cancer. Kidney renal clear cell carcinoma (KIRC), which accounts for more than 70% of all renal malignant tumour cases, was selected for our analysis.Traditional methods of identifying cancer prognostic markers may not be accurate. Tensor decomposition (TD) is a useful method uncovering the underlying low-dimensional structures in the tensor. The TD-based unsupervised feature extraction method was applied to analyse mRNA and miRNA expression profiles. Biological annotations of the prognostic miRNAs and mRNAs were examined utilizing the pathway and oncogenic signature databases DIANA-miRPath and MSigDB.TD identified the miRNA signatures and the associated genes. These genes were found to be involved in cancer-related pathways, and 23 genes were significantly correlated with the survival of KIRC patients. We demonstrated that the results are robust and not highly dependent upon the databases we selected. Compared with traditional supervised methods tested, TD achieves much better performance in selecting prognostic miRNAs and mRNAs.These results suggest that integrated analysis using the TD-based unsupervised feature extraction technique is an effective strategy for identifying prognostic signatures in cancer studies.

scholarly journals Multiomics data analysis using tensor decomposition based unsupervised feature extraction --Comparison with DIABLO--

2019 ◽  
Author(s):  
Y-h. Taguchi
Keyword(s):  
Feature Extraction ◽  
Data Analysis ◽  
Tensor Decomposition ◽  
Integrated Analysis ◽  
Data Sets ◽  
Data Set ◽  
Advanced Method ◽  
Data Mining Tool ◽  
Mining Tool ◽  
Unsupervised Feature Extraction

AbstractMultiomics data analysis is the central issue of genomics science. In spite of that, there are not well defined methods that can integrate multomics data sets, which are formatted as matrices with different sizes. In this paper, I propose the usage of tensor decomposition based unsupervised feature extraction as a data mining tool for multiomics data set. It can successfully integrate miRNA expression, mRNA expression and proteome, which were used as a demonstration example of DIABLO that is the recently proposed advanced method for the integrated analysis of multiomics data set.

scholarly journals Identification of Candidate Drugs for Heart Failure using Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Integrated Analysis of Gene Expression between Heart Failure and DrugMatrix Datasets

2017 ◽  
Author(s):  
Y-h. Taguchi
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Feature Extraction ◽  
Drug Target ◽  
Drug Targets ◽  
Target Genes ◽  
Expression Profiles ◽  
Tensor Decomposition ◽  
Integrated Analysis ◽  
Unsupervised Feature Extraction

AbstractIdentifying drug target genes in gene expression profiles is not straightforward. Because a drug targets not mRNAs but proteins, mRNA expression of drug target genes is not always altered. In addition, the interaction between a drug and protein can be context dependent; this means that simple drug incubation experiments on cell lines do not always reflect the real situation during active disease. In this paper, I apply tensor decomposition-based unsupervised feature extraction to the integrated analysis of gene expression between heart failure and the DrugMatrix dataset where comprehensive data on gene expression during various drug treatments of rats were reported. I found that this strategy, in a fully unsupervised manner, enables us to identify a combined set of genes and compounds, for which various associations with heart failure were reported.

scholarly journals Universal nature of drug treatment responses in drug-tissue-wide model-animal experiments using tensor decomposition-based unsupervised feature extraction

2020 ◽  
Author(s):  
Y-h. Taguchi ◽  
Turki Turki
Keyword(s):  
Gene Expression ◽  
Feature Extraction ◽  
Drug Treatment ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Tensor Decomposition ◽  
Integrated Analysis ◽  
Model Animal ◽  
Multiple Drugs ◽  
Unsupervised Feature Extraction

ABSTRACTGene expression profiles of tissues treated with drugs have recently been used to infer clinical outcomes. Although this method is often successful from the application point of view, gene expression altered by drugs is rarely analyzed in detail, because of the extremely large number of genes involved. Here, we applied tensor decomposition (TD)-based unsupervised feature extraction (FE) to the gene expression profiles of 24 mouse tissues treated with 15 drugs. TD-based unsupervised FE enabled identification of the common effects of 15 drugs including an interesting universal feature: these drugs affect genes in a gene-group-wide manner and were dependent on three tissue types (neuronal, muscular, and gastroenterological). For each tissue group, TD-based unsupervised FE enabled identification of a few tens to a few hundreds of genes affected by the drug treatment. These genes are distinctly expressed between drug treatments and controls as well as between tissues in individual tissue groups and other tissues. We also validated the assignment of genes to individual tissue groups using multiple enrichment analyses. We conclude that TD-based unsupervised FE is a promising method for integrated analysis of gene expression profiles from multiple tissues treated with multiple drugs in a completely unsupervised manner.

scholarly journals Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ka-Lok Ng ◽  
Y.-H. Taguchi
Keyword(s):  
Feature Extraction ◽  
Cell Carcinoma ◽  
Complex Disease ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Expression Profiles ◽  
Tensor Decomposition ◽  
Renal Clear Cell Carcinoma ◽  
Integrated Analysis ◽  
Unsupervised Feature Extraction

Abstract Cancer is a highly complex disease caused by multiple genetic factors. MicroRNA (miRNA) and mRNA expression profiles are useful for identifying prognostic biomarkers for cancer. Kidney renal clear cell carcinoma (KIRC), which accounts for more than 70% of all renal malignant tumour cases, was selected for our analysis. Traditional methods of identifying cancer prognostic markers may not be accurate. Tensor decomposition (TD) is a useful method uncovering the underlying low-dimensional structures in the tensor. The TD-based unsupervised feature extraction method was applied to analyse mRNA and miRNA expression profiles. Biological annotations of the prognostic miRNAs and mRNAs were examined utilizing the pathway and oncogenic signature databases DIANA-miRPath and MSigDB. TD identified the miRNA signatures and the associated genes. These genes were found to be involved in cancer-related pathways, and 23 genes were significantly correlated with the survival of KIRC patients. We demonstrated that the results are robust and not highly dependent upon the databases we selected. Compared with traditional supervised methods tested, TD achieves much better performance in selecting prognostic miRNAs and mRNAs. These results suggest that integrated analysis using the TD-based unsupervised feature extraction technique is an effective strategy for identifying prognostic signatures in cancer studies.

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