A signaling pathway analysis method based on information divergence

2015 ◽  
Author(s):  
Hang Wei ◽  
Hao-Ran Zheng
Keyword(s):  
Signaling Pathway ◽  
Pathway Analysis ◽  
Analysis Method ◽  
Information Divergence

Identification of perturbed signaling pathways from gene expression data using information divergence

2017 ◽  
Vol 13 (9) ◽  
pp. 1797-1804
Author(s):  
Xinying Hu ◽  
Hang Wei ◽  
Haoran Zheng
Keyword(s):  
Gene Expression ◽  
Probability Distribution ◽  
Signaling Pathways ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Expression Data ◽  
Analysis Method ◽  
Information Divergence

We propose a pathway analysis method based on information divergence and the probability distribution of the regulation capacity.

scholarly journals Icariin promotes osteoblastic differentiation in OVX mice via MAPK signaling pathway revealed by profiling

2018 ◽  
Vol 01 (01) ◽  
pp. 33-41
Author(s):  
Qin Bian ◽  
Shufen Liu ◽  
Yongjian Zhao ◽  
Jianhua Huang ◽  
Ziyin Shen
Keyword(s):  
Bone Mass ◽  
Signaling Pathway ◽  
Pathway Analysis ◽  
Ex Vivo ◽  
Osteoblastic Differentiation ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
The Self ◽  
Self Renewal ◽  
Colony Forming Unit

Objective: Icariin (ICA), an extract from epimedium, has been reported to be effective in promoting bone formation. The objective of the study is to search for the molecular targets of ICA in bone mesenchymal stem cells (bMSCs) from the mice with ovariectomy (OVX)-induced osteoporosis. Methods: Six-month-old Imprinting Control Region (ICR) mice that underwent OVX were treated with ICA. After three months, bone mass was evaluated by microcomputed tomography, morphometry and immunohistological detection. bMSCs were isolated from the femur and tibia to observe the self-renewal and differentiation capacities using colony-forming unit fibroblastic (CFU-F), colony-forming unit adipocyte (CFU-Adipo) and alkaline phosphatase (ALP) staining. In addition, microarray of bMSCs ex vivo was measured two weeks after ICA treatment and analyzed by heatmap and pathway analysis. The signaling pathway was further explored by western blot assay and inhibitors of p38 and ERK: SB203508 and PD98059. Results: [Formula: see text]CT displayed a decrease in bone mass for three months after OVX. ICA treatment increased the trabecular thickness (Tb.Th), osteoblast number while decreased osteoclast number, elevating osteocalcin (OC) protein levels in vivo and facilitating the self-renewal and osteoblastic differentiation of bMSCs ex vivo. Microarray data indicated ICA rescued several gene expressions that were dysregulated by OVX. Pathway analysis revealed that the core genes acted by ICA were highly involved in MAPK signaling pathway. Further study demonstrated ICA suppressed ERK while stimulated p38 phosphorylation to promote osteoblastic differentiation in vitro. Conclusion: ICA promotes osteoblastic differentiation of bMSCs in OVX mice. MAPK signaling pathway might be involved in the process.

IGF signaling pathway analysis of osteosarcomas reveals the prognostic value of pAKT localization

2013 ◽  
Vol 9 (11) ◽  
pp. 1733-1740 ◽  
Author(s):  
Addy CM van de Luijtgaarden ◽  
Melissa HS Roeffen ◽  
Manon A Leus ◽  
Uta E Flucke ◽  
Bart HWB Schreuder ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Pathway Analysis ◽  
Prognostic Value ◽  
Igf Signaling

scholarly journals Mechanisms of Berberine for the Treatment of Atherosclerosis Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-11 ◽  
Author(s):  
Xuejiao Xie ◽  
Xingyu Ma ◽  
Siyu Zeng ◽  
Wansi Tang ◽  
Liucheng Xiao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Foam Cell Formation ◽  
Ppi Network ◽  
The Core ◽  
Ppi Networks ◽  
Kegg Pathway Analysis

Atherosclerosis is a common metabolic disease characterized by lipid metabolic disorder. The processes of atherosclerosis include endothelial dysfunction, new endothelial layer formation, lipid sediment, foam cell formation, plaque formation, and plaque burst. Owing to the adverse effects of first-line medications, it is urgent to discover new medications to deal with atherosclerosis. Berberine is one of the most promising natural products derived from traditional Chinese medicine. However, the panoramic mechanism of berberine against atherosclerosis has not been discovered clearly. In this study, we used network pharmacology to investigate the interaction between berberine and atherosclerosis. We identified potential targets related to berberine and atherosclerosis from several databases. A total of 31 and 331 putative targets for berberine and atherosclerosis were identified, respectively. Then, we constructed berberine and atherosclerosis targets with PPI data. Berberine targets network with PPI data had 3204 nodes and 79437 edges. Atherosclerosis targets network with PPI data had 5451 nodes and 130891 edges. Furthermore, we merged the two PPI networks and obtained the core PPI network from the merged PPI network. The core PPI network had 132 nodes and 3339 edges. At last, we performed functional enrichment analyses including GO and KEGG pathway analysis in David database. GO analysis indicated that the biological processes were correlated with G1/S transition of mitotic cells cycle. KEGG pathway analysis found that the pathways directly associated with berberine against atherosclerosis were cell cycle, ubiquitin mediated proteolysis, MAPK signaling pathway, and PI3K-Akt signaling pathway. After combining the results in context with the available treatments for atherosclerosis, we considered that berberine inhibited inflammation and cell proliferation in the treatment of atherosclerosis. Our study provided a valid theoretical foundation for future research.

Design Graph Theoretical Analysis and In Silico Modeling of Dunaliella Bardawil Biomass Encapsulated N-Succinyl Chitosan Nanoparticles for Enhanced Anticancer Activity

2019 ◽  
Vol 18 (13) ◽  
pp. 1900-1918 ◽  
Author(s):  
Selvaraj Kunjiappan ◽  
Theivendren Panneerselvam ◽  
Balasubramanian Somasundaram ◽  
Murugesan Sankaranarayanan ◽  
Pavadai Parasuraman ◽  
...  
Keyword(s):  
Particle Size ◽  
Molecular Docking ◽  
Anticancer Activity ◽  
Signaling Pathway ◽  
Pathway Analysis ◽  
Chitosan Nanoparticles ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Dunaliella Bardawil ◽  
Ras P21

Purpose: To investigate N-succinyl chitosan nanoparticles (NSC NPs) encapsulation with Dunaliella bardawil (D. bardawil) biomass for high utilization enhanced effectiveness and least side effects for anticancer activity. Methods: The potential bioactive compounds from D. bardawil biomass were encapsulated NSC NPs by ionotropic gelation method and to characterize its molecular shape, particle size, stability and polydispersity index using FTIR, XRD, SEM, TEM and Zetasize Nano analyzer. Signaling pathway analysis, molecular docking study and in vitro anticancer screening were performed on chosen H-Ras P21, 721P and liver cancer cell lines (HepG2), respectively. Results: The D. bardawil biomass majorly contains 6 bioactive compounds such as β-carotene, lutein, zeaxanthin, phytoene, canthaxanthin, and phytofluene were identified by LC-MS. The D. bardawil biomass encapsulated NSC NPs showed an average particle size of 80±5.6 nm in spherical shape, crystalline nature, zeta potential of -32±2.7 mV and polydispersity index of 0.51±0.02. Interestingly, the identified target using graph theoretical signaling pathway analysis and molecular docking study showed strong interaction of NSC NPs in binding pockets of H-Ras P21 protooncogene. At 50μg/mL, NPs displayed 95.60% cytotoxicity in HepG2 cell line. The apoptotic cell cycle analysis showed cell death for 24 h and 48 h representing 13.13% and 47.04%, respectively. Conclusion: The highly cross-linked, biocompatible, biodegradable, nontoxic NSC NPs promising carrier for delivery of bioactive molecules present in the D. bardawil biomass was found to be actively involved in deregulation of cellular growth in targeted cancer cells. Thus active NPs serve as a novel nanodrug to enhance the controlled; site specific drug delivery in the management of cancer.

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