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Gene Expression Regulation

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Galactose-Induced Cataracts in Rats: A Machine Learning Analysis.

International journal of medical sciences
Rat models are widely used to study cataracts due to their cost-effectiveness and prominent physiological and genetic similarities to humans The objective of this study was to identify genes involved in cataractogenesis due to galactose exposure in ...

From Genes to Metabolites: HSP90B1's Role in Alzheimer's Disease and Potential for Therapeutic Intervention.

Neuromolecular medicine
Alzheimer's disease (AD) is a prototypical neurodegenerative disorder, predominantly affecting individuals in the presenile and elderly populations, with an etiology that remains elusive. This investigation aimed to elucidate the alterations in anoik...

Machine learning analysis of gene expression profiles of pyroptosis-related differentially expressed genes in ischemic stroke revealed potential targets for drug repurposing.

Scientific reports
The relationship between ischemic stroke (IS) and pyroptosis centers on the inflammatory response elicited by cerebral tissue damage during an ischemic stroke event. However, an in-depth mechanistic understanding of their connection remains limited. ...

A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions.

Nature communications
Cells are regulated at multiple levels, from regulations of individual genes to interactions across multiple genes. Some recent neural network models can connect molecular changes to cellular phenotypes, but their design lacks modeling of regulatory ...

Investigation and validation of genes associated with endoplasmic reticulum stress in diabetic retinopathy using various machine learning algorithms.

Experimental eye research
BACKGROUND: Diabetic retinopathy (DR) is a common complication of diabetes, with Endoplasmic reticulum stress (ERS) playing a key role in cellular adaptation, injury, or apoptosis, impacting disease pathology. This study aimed to identify early diagn...

Machine learning analysis of FOSL2 and RHoBTB1 as central immunological regulators in knee osteoarthritis synovium.

The Journal of international medical research
BackgroundKnee osteoarthritis is a debilitating disease with a complex pathogenesis. Synovitis, which refers to inflammation of the synovial membrane surrounding the joint, is believed to play an important role in the development and progression of k...

Identifying disease progression biomarkers in metabolic associated steatotic liver disease (MASLD) through weighted gene co-expression network analysis and machine learning.

Journal of translational medicine
BACKGROUND: Metabolic Associated Steatotic Liver Disease (MASLD), encompassing conditions simple liver steatosis (MAFL) and metabolic associated steatohepatitis (MASH), is the most prevalent chronic liver disease. Currently, the management of MASLD i...

TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data.

Nature communications
It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale mult...

Machine learning based identification of anoikis related gene classification patterns and immunoinfiltration characteristics in diabetic nephropathy.

Scientific reports
Anoikis and immune cell infiltration are pivotal factors in the pathophysiological mechanism of diabetic nephropathy (DN), yet a comprehensive understanding of the mechanism is lacking. This work aimed to pinpoint distinctive anoikis-related genes (A...

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.

Nature communications
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are pred...