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Gene Expression Regulation

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Identification and validation of interferon-stimulated gene 15 as a biomarker for dermatomyositis by integrated bioinformatics analysis and machine learning.

Frontiers in immunology
BACKGROUND: Dermatomyositis (DM) is an autoimmune disease that primarily affects the skin and muscles. It can lead to increased mortality, particularly when patients develop associated malignancies or experience fatal complications such as pulmonary ...

Construction of the miRNA/Pyroptosis-Related Molecular Regulatory Axis in Abdominal Aortic Aneurysm: Evidence From Transcriptome Data Combined With Multiple Machine Learning Approaches Followed by Experiment Validation.

Journal of immunology research
Abdominal aortic aneurysm (AAA) represents a permanent and localized widening of the abdominal aorta, posing a potentially lethal risk of aortic rupture. Several recent studies have highlighted the role of pyroptosis, a pro-inflammatory programed ce...

Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.

RNA biology
Regulatory non-coding RNAs (ncRNAs) are increasingly recognized as integral to the control of biological processes. This is often through the targeted regulation of mRNA expression, but this is by no means the only mechanism through which regulatory ...

A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks.

Briefings in bioinformatics
Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is challenging. Her...

Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human lang...

Interpreting cis-regulatory interactions from large-scale deep neural networks.

Nature genetics
The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and interpretation. Current evaluations align DNN predictions with orthogonal experimental data, providin...

Identification of metabolism related biomarkers in obesity based on adipose bioinformatics and machine learning.

Journal of translational medicine
BACKGROUND: Obesity has emerged as a growing global public health concern over recent decades. Obesity prevalence exhibits substantial global variation, ranging from less than 5% in regions like China, Japan, and Africa to rates exceeding 75% in urba...

SDC4 protein action and related key genes in nonhealing diabetic foot ulcers based on bioinformatics analysis and machine learning.

International journal of biological macromolecules
Diabetic foot ulcers (DFU) is a complication associated with diabetes characterised by high morbidity, disability, and mortality, involving chronic inflammation and infiltration of multiple immune cells. We aimed to identify the critical genes in non...

Identification of TXN and F5 as novel diagnostic gene biomarkers of the severe asthma based on bioinformatics and machine learning analysis.

Autoimmunity
Asthma poses a major threat to human health. The aim of this study was to identify genetic markers of severe asthma and analyze the relationship between key genes and immune infiltration. Differentially expressed genes (DEGs) were first screened by d...

A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.

Nucleic acids research
Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene t...