AIMC Topic: Gene Expression Regulation, Neoplastic

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Computational methods using genome-wide association studies to predict radiotherapy complications and to identify correlative molecular processes.

Scientific reports Feb 24, 2017
The biological cause of clinically observed variability of normal tissue damage following radiotherapy is poorly understood. We hypothesized that machine/statistical learning methods using single nucleotide polymorphism (SNP)-based genome-wide associ...
Male Middle Aged Genome-Wide Association Study Cohort Studies Polymorphism, Single Nucleotide Machine Learning Prognosis Aged Biomarkers, Tumor Rectum Hemorrhage Erectile Dysfunction Radiation Tolerance Gamma Rays Gene Expression Regulation, Neoplastic Signal Transduction Neoplasm Proteins Prostatic Neoplasms Prostate Humans
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Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues.

Scientific reports Dec 21, 2016
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a com...
RNA, Messenger Gene Expression Regulation, Neoplastic Gene Expression Profiling Protein Domains Signal Transduction Real-Time Polymerase Chain Reaction Amino Acid Motifs Humans Cluster Analysis Liver Neoplasms GTPase-Activating Proteins Machine Learning Carcinoma, Hepatocellular Dishevelled Proteins Algorithms Computational Biology Phylogeny
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Automated Detection of Cancer Associated Genes Using a Combined Fuzzy-Rough-Set-Based F-Information and Water Swirl Algorithm of Human Gene Expression Data.

PloS one Dec 9, 2016
This study describes a novel approach to reducing the challenges of highly nonlinear multiclass gene expression values for cancer diagnosis. To build a fruitful system for cancer diagnosis, in this study, we introduced two levels of gene selection su...
Humans Gene Expression Profiling Fuzzy Logic Algorithms ROC Curve Reproducibility of Results Genetic Testing Genetic Predisposition to Disease Neoplasms Monte Carlo Method Gene Expression Regulation, Neoplastic Oligonucleotide Array Sequence Analysis
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The method for breast cancer grade prediction and pathway analysis based on improved multiple kernel learning.

Journal of bioinformatics and computational biology Nov 29, 2016
Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer gra...
Humans Machine Learning Algorithms Gene Expression Regulation, Neoplastic Signal Transduction Support Vector Machine DNA Methylation Neoplasm Grading Databases, Factual Female Breast Neoplasms Genomics
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Random Subspace Aggregation for Cancer Prediction with Gene Expression Profiles.

BioMed research international Nov 24, 2016
. Precisely predicting cancer is crucial for cancer treatment. Gene expression profiles make it possible to analyze patterns between genes and cancers on the genome-wide scale. Gene expression data analysis, however, is confronted with enormous chall...
Databases, Nucleic Acid Gene Expression Profiling Gene Expression Regulation, Neoplastic Models, Genetic Humans Predictive Value of Tests Machine Learning Animals Neoplasms
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Adaptive Dimensionality Reduction with Semi-Supervision (AdDReSS): Classifying Multi-Attribute Biomedical Data.

PloS one Jul 15, 2016
Medical diagnostics is often a multi-attribute problem, necessitating sophisticated tools for analyzing high-dimensional biomedical data. Mining this data often results in two crucial bottlenecks: 1) high dimensionality of features used to represent ...
Ovarian Neoplasms Prostatic Neoplasms Prostate Breast Pattern Recognition, Automated Ovary Mitosis Male Diagnosis, Computer-Assisted Image Processing, Computer-Assisted Gene Expression Regulation, Neoplastic Artificial Intelligence Proteomics Algorithms Humans Female Breast Neoplasms
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Ensemble Feature Learning of Genomic Data Using Support Vector Machine.

PloS one Jun 15, 2016
The identification of a subset of genes having the ability to capture the necessary information to distinguish classes of patients is crucial in bioinformatics applications. Ensemble and bagging methods have been shown to work effectively in the proc...
Humans Algorithms Colonic Neoplasms Data Mining Child Female Information Dissemination Genomics Reproducibility of Results Leukemia Computational Biology Breast Neoplasms Gene Expression Regulation, Neoplastic Gene Expression Profiling Support Vector Machine
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Network stratification analysis for identifying function-specific network layers.

Molecular bioSystems Feb 16, 2016
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
Gene Expression Regulation, Fungal Transcription, Genetic Gene Expression Regulation, Neoplastic Signal Transduction Cluster Analysis Models, Biological Neural Networks, Computer Algorithms Disease Progression Gene Expression Profiling Liver Neoplasms Carcinoma, Hepatocellular Protein Interaction Maps Gene Regulatory Networks Computational Biology Humans
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Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory.

BMC bioinformatics Jan 11, 2016
BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the pharmaceutical industry for ident...
Carcinoma, Non-Small-Cell Lung Neoplasm Proteins Drug Repositioning Microarray Analysis Lung Neoplasms Gene Expression Regulation, Neoplastic Signal Transduction Models, Theoretical Humans Machine Learning Algorithms Drug Discovery Antineoplastic Agents
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Serum Dickkopf-1 levels as a clinical and prognostic factor in patients with bladder cancer.

Genetics and molecular research : GMR Dec 28, 2015
Dickkopf-1 (DKK-1) is a secreted protein that inhibits Wnt signaling. However, the clinical significance and prognostic value of serum DKK-1 levels have not been previously investigated in bladder cancer in Chinese patients. Blood samples were taken ...
Urinary Bladder Neoplasms Intercellular Signaling Peptides and Proteins Adult Wnt Signaling Pathway Humans Biomarkers, Tumor Proportional Hazards Models Prognosis Male Kaplan-Meier Estimate Female Middle Aged Aged Gene Expression Regulation, Neoplastic
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