Retraction Note: detangling PPI networks to uncover functionally meaningful clusters

Hall-Swan, Sarah; Crawford, Jake; Newman, Rebecca; Cowen, Lenore

doi:10.1186/s12918-018-0641-3

Cited by 1 publication

(1 citation statement)

References 1 publication

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, protein interaction network maps were constructed for differentially expressed proteins based on protein interaction relationships in STRING or IntAct databases using CytoScape software. In protein-protein interaction networks, highly aggregated proteins may often have the same or similar functions and perform biological functions through synergistic interactions [58,59]. Therefore, based on the principle of topology identification, the proteins with high aggregation in the interactions network graph are classified into different clusters.…”

Section: Discussionmentioning

confidence: 99%

Proteomic comparison between physiological degeneration and needle puncture model of disc generation disease

Zhou

Yang

et al. 2022

Eur Spine J

View full text Add to dashboard Cite

Background The completeness of the intervertebral disc proteome is fundamental to the integrity and functionality of the intervertebral disc. Methods The 20 experimental rats were placed into two groups randomly, normal group (NG) and acupuncture pathological degeneration group-2 weeks (APDG-2w). The ten 24-month-old rats were grouped into physiological degeneration group (PDG). Magnetic resonance imaging, X-ray examination, histological staining (hematoxylin & eosin, safranin-O cartilage, and alcian blue staining), and immunohistochemical examination were carried out for assessing the degree of disc degradation. Intervertebral disc was collected, and protein composition was determined by LC- MS, followed by bioinformatic analysis including significance analysis, subcellular localization prediction, protein domain prediction, GO function and KEGG pathway analysis, and protein interaction network construction. LC-PRM was done for protein quantification. Results Physiological degeneration and especially needle puncture decreased T2 signal intensity and intervertebral disc height. Results from hematoxylin & eosin, safranin-O, and alcian blue staining revealed that the annulus fibrosus apparently showed the wavy and collapsed fibrocartilage lamellas in APDG-2w and PDG groups. The contents of the nucleus pulposus were decreased in physiological degeneration group and APDG-2w group compared with NG. Results from immunohistochemical analysis suggested the degeneration of intervertebral disc and inflammation in APDG-2w and PDG groups. The protein composition and expression between needle puncture rat models and the physiological degeneration group showed significant difference. Conclusions Our studies produced point-reference datasets of normal rats, physiological degeneration rats, and needle puncture rat models, which is beneficial to subsequent pathological studies. There is differential expression of protein expression in degenerative discs with aging and acupuncture, which may be used as a potential discriminating index for different intervertebral degenerations.

show abstract

Section: Discussionmentioning

confidence: 99%