AIMC Topic: Protein Interaction Maps

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Black pepper knowledge base (BlackPepKB): a centralized web resource for functional genomics of black pepper (Piper nigrum L.).

BMC genomics
BACKGROUND: Black pepper (Piper nigrum L.) is a highly valued spice crop with significant economic, medicinal, and cultural importance. While genomic and transcriptomic data for black pepper have rapidly accumulated in recent years, there is currentl...

Identification and validation of aryl hydrocarbon receptor-associated hub genes in ulcerative colitis via integrated bioinformatics analysis.

Human genomics
OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease, continues to pose substantial challenges in both diagnosis and treatment. The aryl hydrocarbon receptor (AhR) plays a pivotal role in intestinal immune regulation; however, its...

Mapping Context-Aware Phosphosite Regulation of Protein-Protein Interactions Using Deep Learning and Pan-Cancer Proteomics.

Journal of chemical information and modeling
Phosphorylation dynamically orchestrates the protein-protein interaction (PPI) network that governs cellular signaling, and its dysregulation frequently drives malignant transformation and neurodegeneration. We present PhosPPI-SEQ, an interpretable d...

Identification of early warning biomarkers for type 4 cardio-renal syndrome based on bioinformatics analysis and secreted proteins.

Scientific reports
Chronic kidney disease (CKD) can induce chronic heart failure (CHF), a condition referred to as type 4 cardiorenal syndrome (CRS4). The pathophysiological mechanisms remain unclear, and suitable early warning biomarkers for CHF in CKD patients are la...

Neutrophil extracellular trapping network-associated biomarkers in liver fibrosis: machine learning and experimental validation.

Journal of translational medicine
BACKGROUND: The diagnostic and therapeutic potential of neutrophil extracellular traps (NETs) in liver fibrosis (LF) has not been fully explored. We aim to screen and verify NETs-related liver fibrosis biomarkers through machine learning.

Comprehensive identification of immune-related biomarkers and therapeutic targets in preeclampsia: integrative bioinformatics and experimental validation.

BMC pregnancy and childbirth
BACKGROUND: Preeclampsia (PE) is a serious hypertensive complication during pregnancy characterized by immune dysregulation and vascular dysfunction, however, the precise molecular mechanisms and effective therapeutic strategies remain unclear. This ...

Discovering periodontitis biomarkers and therapeutic targets through bioinformatics and ensemble learning analysis.

Scientific reports
Periodontitis, a prevalent inflammatory disease, leads to the progressive destruction of periodontal tissues and poses significant systemic health risks. Despite its widespread impact, the molecular mechanisms driving periodontitis remain poorly unde...

Machine learning-based transcriptomic analysis identifies NAMPT and SAT1 as potential biomarkers and therapeutic targets in ferroptosis-associated rheumatoid arthritis.

PloS one
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune disease with chronic presentation, involving symmetric joints and systemic involvement. Ferroptosis is iron-dependent programmed cell death through lipid peroxide accumulation, implicated in infl...

Identification of genes related to the effects of bicalutamide and zoladex on benign prostatic hyperplasia.

Scientific reports
Existing research indicates that bicalutamide and zoladex show significant potential in treating prostate cancer. However, in the clinical application of treating benign prostatic hyperplasia (BPH), it is limited due to relatively severe side effects...

A graph neural network-based approach for predicting SARS-CoV-2-human protein interactions from multiview data.

PloS one
The COVID-19 pandemic has demanded urgent and accelerated action toward developing effective therapeutic strategies. Drug repurposing models (in silico) are in high demand and require accurate and reliable molecular interaction data. While experiment...