AIMC Topic: Transcriptome

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Adipose tissue gene expression and longitudinal clinical phenotypes are early biomarkers of lipid-regulating drug usage.

Scientific reports
Cardiovascular disease progression is characterised by the dysregulation of lipid metabolism and pro-atherogenic effects of adipose tissue signalling. Recent findings from the analysis of transcriptomic data in bulk tissue has enabled these insights ...

Utility of the continuous spectrum formed by pathological states in characterizing disease properties.

NPJ systems biology and applications
Understanding diseases as the result of continuous transitions from a healthy system is more realistic than understanding them as discrete states. Here, we designed the spectrum formation approach (SFA), a machine learning-based method that extracts ...

Integrative analysis of transcriptome and metabolome profiles reveals immune-metabolic alterations in pulmonary sarcoidosis.

Metabolomics : Official journal of the Metabolomic Society
BACKGROUND: Pulmonary sarcoidosis, a disease of unknown etiology, is characterized by the presence of noncaseating granulomas in lung parenchyma. This present study combines metabolomic and transcriptomic data to determine the metabolic and different...

Integrated single-cell and clinical transcriptomic analysis identifies blunted glycolytic activation as a hallmark of maladaptive repair in renal ischemia-reperfusion.

Renal failure
Acute kidney injury (AKI) is a common and increases risk of chronic kidney disease (CKD). While mitochondrial dysfunction drives maladaptive repair, the role of glycolysis in renal recovery remains unclear. Here, we integrated single-cell transcripto...

Immune metabolic changes identify causal candidate genes and enable diagnostic frameworks in MAFLD.

Scientific reports
Metabolic dysfunction-associated fatty liver disease (MAFLD), a global epidemic affecting 25% of adults, is driven by immune-metabolic dysregulation, yet the causal mechanisms linking immune cell-specific gene perturbations to disease progression rem...

Investigating potential biomarkers associated with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis using Mendelian randomization and transcriptomic analysis.

Arthritis research & therapy
BACKGROUND: Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is an autoimmune disorder characterized by multi-organ involvement. Early identification and accurate diagnosis of AAV is crucial for improving prognosis. However, res...

Stacking ensemble learning models diagnose pulmonary infections using host transcriptome data from metatranscriptomics.

Scientific reports
The prompt diagnosis of pulmonary infections with unknown etiology in patients in severe condition remains a challenge due to the lack of rapid and effective diagnostic methods. While metatranscriptomic sequencing offers a powerful approach, its clin...

Integrative machine learning and RT-qPCR analysis identify key stress-responsive genes in Thermus thermophilus HB8.

Genetica
Bacteria are constantly exposed to diverse environmental stresses, necessitating complex adaptive mechanisms for survival. Thermus thermophilus, a thermophilic extremophile, serves as an excellent model for investigating these responses due to its re...

Ferroptosis-related hub genes and immune cell dynamics as diagnostic biomarkers in age-related macular degeneration.

European journal of medical research
BACKGROUND: Age-related Macular Degeneration (AMD) is widely acknowledged as a principal cause of vision loss in the elderly. Currently, the therapeutic interventions available in clinical practice fail to achieve satisfactory outcomes. Therefore, it...

TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues.

Nature communications
The spatial organization of cells plays a pivotal role in shaping tissue functions and phenotypes in various biological systems and diseased microenvironments. However, the topological principles governing interactions among cell types within spatial...