AIMC Topic: Gene Expression Profiling

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A 21‑gene Support Vector Machine classifier and a 10‑gene risk score system constructed for patients with gastric cancer.

Molecular medicine reports Nov 21, 2019
Gastric cancer (GC) ranks fifth in terms of incidence and third in terms of tumor mortality worldwide. The present study was designed to construct a Support Vector Machine (SVM) classifier and risk score system for GC. The GSE62254 (training set) and...
Humans Cytokines Prognosis Female Angiopoietin-like Proteins A Kinase Anchor Proteins Angiopoietin-Like Protein 1 Membrane Proteins Support Vector Machine Databases, Genetic Carrier Proteins Nerve Tissue Proteins Neoplasm Recurrence, Local Tumor Suppressor Proteins Kaplan-Meier Estimate Middle Aged Gene Expression Profiling Gene Regulatory Networks Gene Expression Regulation, Neoplastic Risk Factors Aged Stomach Neoplasms Male
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Gene expression based survival prediction for cancer patients-A topic modeling approach.

PloS one Nov 15, 2019
Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard ...
Datasets as Topic Kaplan-Meier Estimate Oligonucleotide Array Sequence Analysis Humans Prognosis Neoplasms Gene Expression Profiling Gene Expression Regulation, Neoplastic Natural Language Processing Models, Biological
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DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome.

Scientific reports Nov 11, 2019
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Network...
Neural Networks, Computer Algorithms Reproducibility of Results Neoplasms Humans Gene Expression Regulation, Neoplastic Data Mining Gene Expression Profiling Disease Susceptibility Transcriptome Organ Specificity Deep Learning Pathology, Molecular Computational Biology
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Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data.

PloS one Nov 8, 2019
Several studies have reported mitochondrial dysfunction in rheumatoid arthritis (RA). Many nuclear DNA (nDNA) encoded proteins translocate to mitochondria, but their participation in the dysfunction of this cell organelle during RA is quite unclear. ...
Gene Expression Regulation Gene Ontology Mitochondrial Proteins Humans Oxidative Phosphorylation Gene Expression Profiling Reactive Oxygen Species Synovial Membrane Protein Interaction Maps Models, Biological Apoptosis Arthritis, Rheumatoid Mitochondria Inflammation
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Integrative Deep Learning for Identifying Differentially Expressed (DE) Biomarkers.

Computational and mathematical methods in medicine Nov 2, 2019
As a large amount of genetic data are accumulated, an effective analytical method and a significant interpretation are required. Recently, various methods of machine learning have emerged to process genetic data. In addition, machine learning analysi...
Biomarkers Regression Analysis Gene Expression Profiling Humans Computer Simulation Deep Learning Neural Networks, Computer Female Genomics Breast Neoplasms Software Support Vector Machine Algorithms
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D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference.

Genes Oct 14, 2019
Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene e...
Deep Learning Computational Biology Sequence Analysis, DNA DNA Methylation Humans Machine Learning Gene Expression Profiling Promoter Regions, Genetic Gene Expression Linear Models CpG Islands Gene Expression Regulation
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Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal.

Journal of visualized experiments : JoVE Oct 11, 2019
Differential gene expression analysis is an important technique for understanding disease states. The machine learning algorithm CorEx has shown utility in analyzing differential expression of groups of genes in tumor RNA-seq in a way that may be hel...
Patient Portals Machine Learning Algorithms Precision Medicine Neoplasms Gene Expression Profiling Gene Expression Regulation, Neoplastic RNA Genome Humans
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Identification of a blood-based 12-gene signature that predicts the severity of coronary artery stenosis: An integrative approach based on gene network construction, Support Vector Machine algorithm, and multi-cohort validation.

Atherosclerosis Oct 9, 2019
BACKGROUND AND AIMS: We aimed to identify a blood-based gene expression score (GES) to predict the severity of coronary artery stenosis in patients with known or suspected coronary artery disease (CAD) by integrative use of gene network construction,...
Support Vector Machine Predictive Value of Tests Coronary Stenosis Female Reproducibility of Results Humans Risk Factors Decision Support Techniques China Aged Phenotype Gene Regulatory Networks Severity of Illness Index Retrospective Studies Male Gene Expression Profiling Genetic Predisposition to Disease Transcriptome Middle Aged Nomograms
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Predicting gene regulatory interactions based on spatial gene expression data and deep learning.

PLoS computational biology Sep 17, 2019
Reverse engineering of gene regulatory networks (GRNs) is a central task in systems biology. Most of the existing methods for GRN inference rely on gene co-expression analysis or TF-target binding information, where the determination of co-expression...
Animals Computational Biology Gene Expression Profiling Databases, Genetic Deep Learning Drosophila Gene Regulatory Networks Eye
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Machine learning predicts putative hematopoietic stem cells within large single-cell transcriptomics data sets.

Experimental hematology Sep 9, 2019
Hematopoietic stem cells (HSCs) are an essential source and reservoir for normal hematopoiesis, and their function is compromised in many blood disorders. HSC research has benefitted from the recent development of single-cell molecular profiling tech...
Machine Learning Animals Gene Expression Profiling Transcriptome Mice Sequence Analysis, RNA Mice, Knockout Hematopoietic Stem Cells
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