AIMC Topic: Gene Expression Regulation

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Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Nucleic acids research Nov 29, 2016
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF b...
Primary Cell Culture Chromatin Chromatin Assembly and Disassembly Human Embryonic Stem Cells Organ Specificity Protein Binding K562 Cells Histones Binding Sites Transcription Factors Hep G2 Cells Cell Line Humans Principal Component Analysis Machine Learning DNA Algorithms CD4-Positive T-Lymphocytes Cell Line, Tumor Hepatocytes Gene Expression Regulation
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Apoptosis of rat hepatic stellate cells induced by diallyl trisulfide and proteomics profiling in vitro.

Canadian journal of physiology and pharmacology Nov 18, 2016
Diallyl trisulfide (DATS), a major garlic derivative, inhibits cell proliferation and triggers apoptosis in a variety of cancer cell lines. However, the effects of DATS on hepatic stellate cells (HSCs) remain unknown. The aim of this study was to ana...
Apoptosis Animals Allyl Compounds Cell Survival Rats Cell Cycle Hepatic Stellate Cells Garlic Proteomics Sulfides Cell Proliferation Gene Expression Regulation
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Comprehensive analysis of epigenetically regulated genes in anergic T cells.

Cellular immunology Nov 2, 2016
T cell anergy is one of the important mechanisms for immune tolerance. The results of many studies investigating the mechanism for T cell anergy induction have revealed that the expression of several genes was up-regulated in anergic T cells. It has ...
Humans Gene Expression Regulation Th1 Cells Gene Ontology Clonal Anergy Immune Tolerance Animals Transcriptome Mice Epigenesis, Genetic DNA Methylation
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Symbiont modulates expression of specific gene categories in Angomonas deanei.

Memorias do Instituto Oswaldo Cruz Oct 3, 2016
Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of the evolutionary process of vital cell functions such as respiration and photosyn...
Transcriptome Genomics Bacteria Genome, Protozoan Gene Expression Regulation Humans Animals Gene Expression Profiling Trypanosomatina Gene Ontology RNA, Protozoan Symbiosis Genes, Protozoan
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Adaptations to excess choline in insulin resistant and Pcyt2 deficient skeletal muscle.

Biochemistry and cell biology = Biochimie et biologie cellulaire Sep 6, 2016
It was hypothesized that choline supplementation in insulin resistant (IR) CTP:phosphoethanolamine cytidylyltransferase deficient (Pcyt2) mice would ameliorate muscle function by remodeling glucose and fatty acid (FA) metabolism. Pcyt2 mice either re...
Gene Expression Regulation fas Receptor PPAR alpha Animals Triglycerides Mice Microtubule-Associated Proteins Insulin Resistance Diacylglycerol O-Acyltransferase Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha Stearoyl-CoA Desaturase Glucose Signal Transduction Insulin Receptor Substrate Proteins Lipogenesis Muscle, Skeletal Organic Cation Transport Proteins Fatty Acids Adaptation, Physiological Mice, Knockout RNA Nucleotidyltransferases Administration, Oral Carnitine O-Palmitoyltransferase Sterol Regulatory Element Binding Protein 1 Choline
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Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.

BMC systems biology Aug 1, 2016
BACKGROUND: Gene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far from the gene promoters are often responsible for mediating...
Neural Networks, Computer Cell Line, Tumor Computational Biology Gene Expression Regulation Histones Humans Enhancer Elements, Genetic
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Batch Mode TD($\lambda$ ) for Controlling Partially Observable Gene Regulatory Networks.

IEEE/ACM transactions on computational biology and bioinformatics Jul 28, 2016
External control of gene regulatory networks (GRNs) has received much attention in recent years. The aim is to find a series of actions to apply to a gene regulation system making it avoid its diseased states. In this work, we propose a novel method ...
Least-Squares Analysis Gene Expression Regulation Yeasts Humans Machine Learning Algorithms Computer Simulation Melanoma Gene Regulatory Networks Computational Biology
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Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models.

International journal of molecular sciences May 20, 2016
Stroke is one of the most common causes of death, only second to heart disease. Molecular investigations about stroke are in acute shortage nowadays. This study is intended to explore a gene expression profile after brain ischemia reperfusion. Meta-a...
Gene Ontology Oligonucleotide Array Sequence Analysis Mice Rats Disease Models, Animal Infarction, Middle Cerebral Artery Humans Gene Expression Regulation Animals Gene Expression Profiling
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g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Nucleic acids research Apr 20, 2016
Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene ...
Vertebrates Transcription Factors Internet Humans Plants Gene Expression Regulation Animals Fungi Molecular Sequence Annotation Gene Expression Profiling Insecta Gene Ontology User-Computer Interface Binding Sites Protein Binding Computer Graphics
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Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression.

Molecular autism Mar 15, 2016
BACKGROUND: Intellectual disability (ID), autism, and epilepsy share frequent yet variable comorbidities with one another. In order to better understand potential genetic divergence underlying this variable risk, we studied genes responsible for mono...
Nerve Tissue Proteins Epilepsy Syndrome Cell Nucleus Gene Expression Regulation Autistic Disorder Risk Gene Ontology Neurogenesis Protein Interaction Maps Humans Intellectual Disability Genetic Association Studies Autism Spectrum Disorder Epigenomics Body Patterning Comorbidity Nuclear Proteins Databases, Genetic Chromatin Assembly and Disassembly Penetrance
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