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Gene Expression Regulation

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Comprehensive analysis of epigenetically regulated genes in anergic T cells.

Cellular immunology
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 ...

Symbiont modulates expression of specific gene categories in Angomonas deanei.

Memorias do Instituto Oswaldo Cruz
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...

Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.

BMC systems biology
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...

Batch Mode TD($\lambda$ ) for Controlling Partially Observable Gene Regulatory Networks.

IEEE/ACM transactions on computational biology and bioinformatics
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 ...

Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models.

International journal of molecular sciences
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...

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Nucleic acids research
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 ...

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

BMC bioinformatics
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...