AIMC Topic: Gene Expression Profiling

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Multiomic integration reveals subtype-specific predictors of neoadjuvant treatment response in breast cancer.

Science advances
Neoadjuvant therapy has been widely used in breast cancer, but treatment response varies among individuals. We conducted multiomic profiling on tumor samples from 149 Chinese patients with breast cancer across ERHER2, ERHER2, and ERHER2 subtypes, cat...

Identification of key genes as diagnostic biomarkers for IBD using bioinformatics and machine learning.

Journal of translational medicine
BACKGROUND: The pathogenesis of inflammatory bowel disease (IBD) involves complex molecular mechanisms, and achieving clinical remission remains challenging. This study aims to identify IBD-potential biomarkers, analyze their correlation with immune ...

Machine learning-assisted multi-dimensional transcriptomic analysis of cytoskeleton-related molecules and their relationship with prognosis in hepatocellular carcinoma.

Scientific reports
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, with a poor prognosis due to its aggressive nature and limited treatment options. Cytoskeletal dynamics play a critical role in tumor progression, but the prognostic...

Exploring the impact of neutrophils on lung adenocarcinoma using Mendelian randomization and transcriptomic study.

Scientific reports
Tumor immune microenvironment plays a crucial role in determining the prognosis of lung adenocarcinoma (LUAD), with the interaction of immune cells within this microenvironment contributing to a poorer prognosis. We sought to investigate the causal r...

Machine learning-based integration identifies plasma cells-related gene signature ST6GAL1 in idiopathic pulmonary fibrosis.

BMC pulmonary medicine
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a rare, progressive, and fibrotic disease with poor prognosis that lacks treatment options. As a major component of the lung adaptive immune system, plasma cells play a crucial regulatory role during...

Cohesive data analysis for the identification of prognostic hub genes and significant pathways associated with HER2 + and TN breast cancer types.

Scientific reports
Breast cancer is the most prevalent and lethal form of cancer being the utmost common medical concern of women. Breast cancer etiology implicates numerous cellular protein receptors such as estrogen receptors (ER), progesterone receptors (PR), and hu...

Identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis through multiomics integration and machine learning.

Scientific reports
Knee osteoarthritis (KOA) is a prevalent degenerative joint disorder, yet its underlying molecular mechanisms remain puzzling. This study aimed to uncover the genes with a causal relationship to KOA using Mendelian randomization (MR), transcriptomic ...

Deep molecular profiling of synovial biopsies in the STRAP trial identifies signatures predictive of treatment response to biologic therapies in rheumatoid arthritis.

Nature communications
Approximately 40% of patients with rheumatoid arthritis do not respond to individual biologic therapies, while biomarkers predictive of treatment response are lacking. Here we analyse RNA-sequencing (RNA-Seq) of pre-treatment synovial tissue from the...

Prioritizing perturbation-responsive gene patterns using interpretable deep learning.

Nature communications
Spatially resolved transcriptomics enables mapping of multiplexed gene expression within tissue contexts. While existing methods prioritize spatially variable genes within a single slice, few address identifying genes with differential spatial expres...

Cross modality learning of cell painting and transcriptomics data improves mechanism of action clustering and bioactivity modelling.

Scientific reports
In drug discovery, different data modalities (chemical structure, cell biology, quantum mechanics, etc.) are abundant, and their integration can help with understanding aspects of chemistry, biology, and their interactions. Within cell biology, cell ...