Prediction of Molecular Signature, Potential Biomarkers, and Molecular Pathways Associated with Membranous Nephropathy Based on Protein-Protein Interactions

Taherkhani, Amir; Kalantari, Shiva; Nafar, M

doi:10.24875/ric.18002551

Cited by 7 publications

(7 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The function of RXR-A is in line with that of retinoic acid R-α, which activates naïve CD4+ T cells (Chambon 1996 ; Taherkhani et al. 2018 ). Furthermore, the differentiation of naïve CD4 + T cells may contribute to reducing the degree of severity of ALI and uncontrolled inflammation (Taherkhani et al.…”

Section: Discussionmentioning

confidence: 95%

See 1 more Smart Citation

Metabolomics coupled with network pharmacology study on the protective effect of Keguan-1 granules in LPS-induced acute lung injury

Chen

Zhou

Zhao

et al. 2022

Pharmaceutical Biology

View full text Add to dashboard Cite

Context Keguan-1 (KG-1) plays a vital role in enhancing the curative effects, improving quality of life, and reducing the development of acute lung injury (ALI). Objective To unravel the protective effect and underlying mechanism of KG-1 against ALI. Materials and methods C57BL/6J mice were intratracheally instilled with lipopolysaccharide to establish the ALI model. Then, mice in the KG-1 group received a dose of 5.04 g/kg for 12 h. The levels of proinflammatory cytokines, chemokines, and pathological characteristics were determined to explore the effects of KG-1. Next, untargeted metabolomics was used to identify the differential metabolites and involved pathways for KG-1 anti-ALI. Network pharmacology was carried out to predict the putative active components and drug targets of KG-1 anti-ALI. Results KG-1 significantly improved the levels of TNF-α (from 2295.92 ± 529.87 pg/mL to 1167.64 ± 318.91 pg/mL), IL-6 (from 4688.80 ± 481.68 pg/mL to 3604.43 ± 382.00 pg/mL), CXCL1 (from 4361.76 ± 505.73 pg/mL to 2981.04 ± 526.18 pg/mL), CXCL2 (from 5034.09 ± 809.28 pg/mL to 2980.30 ± 747.63 pg/mL), and impaired lung histological damage. Untargeted metabolomics revealed that KG-1 significantly regulated 12 different metabolites, which mainly related to lipid, amino acid, and vitamin metabolism. Network pharmacology showed that KG-1 exhibited anti-ALI effects through 17 potentially active components acting on seven putative drug targets to regulate four metabolites. Discussion and conclusions This work elucidated the therapeutic effect and underlying mechanism by which KG-1 protects against ALI from the view of the metabolome, thus providing a scientific basis for the usage of KG-1.

show abstract

Section: Discussionmentioning

confidence: 95%

“…Furthermore, the differentiation of naïve CD4 + T cells may contribute to reducing the degree of severity of ALI and uncontrolled inflammation (Taherkhani et al. 2018 ). The CYP1A enzymes are protective against hyperoxic lung injury (Callaway et al.…”

Section: Discussionmentioning

confidence: 99%

Metabolomics coupled with network pharmacology study on the protective effect of Keguan-1 granules in LPS-induced acute lung injury

Chen

Zhou

Zhao

et al. 2022

Pharmaceutical Biology

View full text Add to dashboard Cite

show abstract

“…A complicated approach named "genome-wide ranking-and-recovery approach" is applied by iRegulon to illustrate the motifs, consisting of a set of genes and their common regulator. Each regulator's normalized enrichment score (NES) was also determined, reflecting the associated motif's significance [29][30][31].…”

Section: Grn Constructionmentioning

confidence: 99%

Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study

et al. 2021

Self Cite

View full text Add to dashboard Cite

Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.

show abstract

“…e iRegulon plugin was used for the detection of potential TFs for the hub genes [18]. In this regard, the TFs with a normalized enrichment score (NES) >3 were considered statistically significant [28]. Furthermore, the validated upstream miRNAs for the hub genes were identified using the MiRWalk 2.0 database, available at https://zmf.…”

Section: Grn Constructionmentioning

confidence: 99%

Potential Biomarkers and Signaling Pathways Associated with the Pathogenesis of Primary Ameloblastoma: A Systems Biology Approach

Bayat

Mirzaeian

Taherkhani

2022

International Journal of Dentistry

Self Cite

View full text Add to dashboard Cite

Objective. Ameloblastoma is a benign odontogenic tumor that may lead to ameloblastic carcinoma. is study aimed to determine potential signaling pathways and biological processes, critical genes and their regulating transcription factors (TFs), and miRNAs, as well as protein kinases involved in the etiology of primary ameloblastoma. Methods. e dataset GSE132472 was obtained from the GEO database, and multivariate statistical analyses were applied to identify di erentially expressed genes (DEGs) in primary ameloblastoma tissues compared to the corresponding normal gingiva samples. A protein-protein interaction (PPI) map was built using the STRING database. e Cytoscape software identi ed signi cant modules and the hub genes within the PPI network. Gene Ontology annotation and signaling pathway analyses were executed by employing the DAVID and Reactome databases, respectively. Signi cant TFs and miRNAs acting on the hub genes were identi ed using the iRegulon plugin and MiRWalk 2.0 database, respectively. A protein kinase enrichment analysis was conducted using the online Kinase Enrichment Analysis 2 (KEA2) web server. e approved drugs acting on the hub genes were also found. Results. A total of 1,629 genes were di erentially expressed in primary ameloblastoma (P value <0.01 and |Log2FC| > 1). HRAS, CDK1, MAPK3, ERBB2, COL1A1, CYCS, and BRCA1 demonstrated high degree and betweenness centralities in the PPI network. E2F4 was the most signi cant TF acting on the hub genes. BTK was the protein kinase signi cantly enriched by the TFs. Cholesterol biosynthesis was considerably involved in primary ameloblastoma. Conclusions. is study provides an intuition into the potential mechanisms involved in the etiology of ameloblastoma.

show abstract

Prediction of Molecular Signature, Potential Biomarkers, and Molecular Pathways Associated with Membranous Nephropathy Based on Protein-Protein Interactions

Abstract: Omics data integration and systems biology analysis on the level of interaction networks provide a powerful approach for identification of pathway-specific biomarkers for MN.

Cited by 7 publications

References 40 publications

Metabolomics coupled with network pharmacology study on the protective effect of Keguan-1 granules in LPS-induced acute lung injury

Metabolomics coupled with network pharmacology study on the protective effect of Keguan-1 granules in LPS-induced acute lung injury

Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study

Potential Biomarkers and Signaling Pathways Associated with the Pathogenesis of Primary Ameloblastoma: A Systems Biology Approach

Contact Info

Product

Resources

About