Identification of mitophagy-related hub genes during the progression of spinal cord injury by integrated multinomial bioinformatics analysis
Notice bibliographique
Résumé
Spinal cord injury (SCI) is a disturbance of peripheral and central nerve conduction that causes disability in sensory and motor function. Currently, there is no effective treatment for SCI. Mitophagy plays a vital role in mitochondrial quality control during various physiological and pathological processes. The study aimed to elucidate the role of mitophagy and identify potential mitophagy-related hub genes in SCI pathophysiology. Two datasets (GSE15878 and GSE138637) were analyzed. Firstly, the differentially expressed genes (DEGs) were identified and mitophagy-related genes were obtained from GeneCards, then the intersection between SCI and mitophagy-related genes was determined. Next, we performed gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), protein-protein interaction network (PPI network), least absolute shrinkage and selection operator (LASSO), and cluster analysis to identify and define the hub genes in SCI. Finally, the link between hub genes and infiltrating immune cells was investigated and the potential transcriptional regulation/small molecular compounds to target hub genes were predicted. In total, SKP1 and BAP1 were identified as hub genes of mitophagy-related DEGs during SCI development and regulatory T cells (Tregs)/resting NK cells/activated mast cells may play an essential role in the progression of SCI. LINC00324 and SNHG16 may regulate SKP1 and BAP1, respectively, through miRNAs. Eleven and eight transcriptional factors (TFs) regulate SKP1 and BAP1, respectively, and six small molecular compounds target BAP1. Then, the mRNA expression levels of BAP1 and SKP1 were detected in the injured sites of spinal cord of SD rats at 6 h and 72 h after injury using RT-qPCR, and found that the level were decreased. Therefore, the pathways of mitophagy are downregulated during the pathophysiology of SCI, and SKP1 and BAP1 could be accessible targets for diagnosing and treating SCI. • The hub genes of mitophagy-related DEGs SKP1 and BAP1 were predicted and validated. • Immune response in SCI were predicted and maybe regulated by the BAP1 and SKP1. • The regulatory relationship of non-coding RNAs/TFs/compounds on SKP1 and BAP1 were predicted. Through Integrated Multinomial Bioinformatics Analysis, we found mitophagy related genes were taken part in the progression of SCI, and the potential hub genes SKP1 and BAP1 were identified, the transcriptional regulation and targeted small molecular compound were predicted.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».