Plasma Membrane Targeting of Protocadherin 15 Is Regulated by the Golgi-Associated Chaperone Protein PIST by Hongyun Nie, Yueyue Liu, Xiaolei Yin, Huiren Cao, Yanfei Wang, Wei Xiong, Yushuang Lin, Zhigang Xu

“…Here we show that PIST, a Golgi-associated, PDZ domain-containing protein, interacts with PCDH15. The interaction is mediated by the PDZ domain of PIST and the C-terminal PDZ domain-binding interface (PBI) of PCDH15. …”
Get full text

Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease by Seokjin Ham, Yeon-Mok Oh, Tae-Young Roh

“…Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. …”
Get full text

DYRK1A (Dual-Specificity Tyrosine-Phosphorylated and -Regulated Kinase 1A): A Gene with Dosage Effect During Development and Neurogenesis by M. Dierssen, M. Martínez de Lagrán

“…The large number of protein interaction and putative substrates described for DYRK1A suggest multiple pathways and functions to be involved in its developmental function. …”
Get full text

Activation Mechanism of LRRK2 and Its Cellular Functions in Parkinson’s Disease by Katharina E. Rosenbusch, Arjan Kortholt

“…LRRK2 belongs to the group of Roco proteins which are characterized by the presence of a Ras-like G-domain (Roc), a C-terminal of Roc domain (COR), a kinase, and several protein-protein interaction domains. Roco proteins exhibit a complex activation mechanism involving intramolecular signaling, dimerization, and substrate/effector binding. …”
Get full text

The combined use of scRNA-seq and network propagation highlights key features of pan-cancer Tumor-Infiltrating T cells. by Adèle Mangelinck, Elodie Molitor, Ibtissam Marchiq, Lamine Alaoui, Matthieu Bouaziz, Renan Andrade-Pereira, Hélène Darville, Etienne Becht, Céline Lefebvre

“…To overcome noise and sparsity inherent to single cell transcriptomics, we then propagated the gene signatures by diffusion in a protein-protein interaction network using the Patrimony high-throughput computing platform. …”
Get full text

Intraneuronal binding of amyloid beta with reelin-Implications for the onset of Alzheimer's disease. by Asgeir Kobro-Flatmoen, Stig W Omholt

“…In a rat model used to study AD, it was recently shown that in layer II neurons of the anteriolateral entorhinal cortex expressing high levels of the glycoprotein reelin (Re+alECLII neurons), reelin and Aβ engage in a direct protein-protein interaction. If reelin functions as a sink for intracellular Aβ and if the binding to reelin makes Aβ physiologically inert, it implies that reelin can prevent the neuron from being exposed to the harmful effects typically associated with increased levels of oligomeric Aβ. …”
Get full text

Using Network Pharmacology to Explore the Mechanism of Panax notoginseng in the Treatment of Myocardial Fibrosis by Jingxue Han, Jingyi Hou, Yu Liu, Peng Liu, Tingting Zhao, Xinwei Wang

“…Targets of MF were then screened to select common targets and construct a protein-protein interaction network. This was followed by Gene Ontology and pathway enrichment analyses. …”
Get full text

TNIP1 in Autoimmune Diseases: Regulation of Toll-like Receptor Signaling by Rambon Shamilov, Brian J. Aneskievich

“…In addition to earlier foundational reports of TNIP1 SNPs in human autoimmune diseases and TNIP1 protein-protein interaction with receptor regulating proteins, more recent studies have identified new potential interaction partners and signaling pathways likely modulated by TNIP1. …”
Get full text

The Identification of Immune-Related Biomarkers for Osteoarthritis Immunotherapy Based on Single-Cell RNA Sequencing Analysis by Zhe Tan, Rong Chen, Hanyu Lin, Hong Wang

“…In addition, the Venn diagram was applied to evaluate the genes that are involved in OA and immune-related genes. The protein-protein interaction analysis was further conducted to explore the hub genes. …”
Get full text

Uncover the Underlying Mechanism of Drug-Induced Myopathy by Using Systems Biology Approaches by Dong Li, Aixin Li, Hairui Zhou, Xi Wang, Peng Li, Sheng Bi, Yang Teng

“…In this study, we curated the comprehensive DIM drug list based on structured labeling products (SPLs) and carried out the analysis based on chemical structure space, drug protein interaction, side effect space, and transcriptomic profiling space. …”
Get full text

Probing SARS-CoV-2 membrane binding peptide via single-molecule AFM-based force spectroscopy by Qingrong Zhang, Raissa S. L. Rosa, Ankita Ray, Kimberley Durlet, Gol Mohammad Dorrazehi, Rafael C. Bernardi, David Alsteens

“…Here, we investigate how the SARS-CoV-2 spike protein interacts with host cell membranes, focusing on a membrane-binding peptide (MBP) located near the TMPRSS2 cleavage site. …”
Get full text

ITGAX promotes gastric cancer progression via epithelial-mesenchymal transition pathway by Jiali Hu, Jing Cao, Shanshan Huang, Yang Chen, Yang Chen

“…Furthermore, we explored the underlying role of ITGAX using Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction networks (PPI) analysis. Our findings reveal that ITGAX promotes gastric cancer progression by driving epithelial-mesenchymal transition pathway (EMT), suggesting its potential as a biomarker for early diagnosis and prognosis in gastric cancer.…”
Get full text

A Network-Based Approach to Explore the Mechanism and Bioactive Compounds of Erzhi Pill against Metabolic Dysfunction-Associated Fatty Liver Disease by Shaojie Huang, Fei Mu, Fei Li, Wenjun Wang, Haixia Chen, Lu Lei, Yang Ma, Yi Ding, Jingwen Wang

“…This was carried out through target prediction, protein-protein interaction (PPI) network construction, gene ontology, KEGG pathway enrichment, and molecular docking. …”
Get full text

Identification of Differentially Expressed Genes in Pituitary Adenomas by Integrating Analysis of Microarray Data by Peng Zhao, Wei Hu, Hongyun Wang, Shengyuan Yu, Chuzhong Li, Jiwei Bai, Songbai Gui, Yazhuo Zhang

“…Gene function analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) networks analysis was conducted to interpret the biological role of those DEGs. …”
Get full text

Identification and Expression Profiling of the BTB Domain-Containing Protein Gene Family in the Silkworm, Bombyx mori by Daojun Cheng, Wenliang Qian, Meng Meng, Yonghu Wang, Jian Peng, Qingyou Xia

“…The BTB domain is a conserved protein-protein interaction motif. In this study, we identified 56 BTB domain-containing protein genes in the silkworm, in addition to 46 in the honey bee, 55 in the red flour beetle, and 53 in the monarch butterfly. …”
Get full text

Bioinformatics analysis of mitochondrial metabolism-related genes demonstrates their importance in renal cell carcinoma by Mohsen Ahmadi, Maryam Motallebinezhad, Pegah Mousavi, Amir Hossein Miladipour, Shamim Fooladgar, Soudeh Ghafouri-Fard, Seyed Amirhossein Fazeli

“…For this purpose, we investigated various aspects of the relationship between mitochondrial metabolism and ccRCC based on analysis of gene network connections and differentially expressed genes, through assessment of protein–protein interaction, mutations, and promoter methylation on the related genes. …”
Get full text

Identification of hub genes and pathogenesis in Kawasaki disease based on bioinformatics analysis by Min Cao, Zhenhu Zhang, Qian Liu, Yuda Zhang

“…Materials and Methods: Gene Expression Omnibus (GEO) datasets GSE68004 and GSE73461 were downloaded, and the differentially expressed genes (DGEs) were taken, along with DEGs enrichment analysis and protein interaction network. Finally, five algorithms in CytoHubba plug-in were applied to obtain hub genes. …”
Get full text

Exosomal insights into ovarian cancer stem cells: revealing the molecular hubs by Kiana Sojoudi, Maryam Solaimani, Hossein Azizi

“…In this study, we used a protein-protein interaction (PPI) network. Using the Clustermaker2 app and the MCODE algorithm, we identified six significant clusters within the network, highlighting regions involved in functional pathways. …”
Get full text

DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features by Omar Barukab, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou

“…It is DNA, which makes a living thing, a living thing. Protein interaction with DNA performs an essential role in regulating DNA functions such as DNA repair, transcription, and regulation. …”
Get full text

Exploring effector protein dynamics and natural fungicidal potential in rice blast pathogen Magnaporthe oryzae. by Jannatul Ferdousy, Tanjin Barketullah Robin, Mst Sanjida Nasrin, Istiak Ahmed, Tawsif Hossain, Md Mehedi Hasan, Mehrab Hassan Soaeb, Md Ahsanul Tamim, Nusrat Jahan Yeasmin, Ummay Habiba, Nadim Ahmed, Nurul Amin Rani, Md Shishir Bhuyian, Suvarna N Vakare, Abu Tayab Moin, Rajesh B Patil, Mohammad Shahadat Hossain

“…Genetic and genomic studies have identified key genes and proteins, such as AvrPik variants and MAX proteins, that are crucial for the pathogen's virulence. These effector proteins interact with specific alleles of the Pik gene family on rice chromosome 11, modulating the host's immune response. …”
Get full text