Visualize omics data on networks with Omics Visualizer, a Cytoscape App

Legeay, Marc; Doncheva, Nadezhda T.; Morris, John H.; Jensen, Lars Juhl

doi:10.12688/f1000research.22280.2

Cited by 47 publications

(47 citation statements)

References 11 publications

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“…Cytoscape is a freely available platform for biological network visualization and analysis that provides a vast array of applications for specialized functions. Two such applications used in the current study are the stringApp 30 , which allowed the direct import of networks from the STRING database into Cytoscape and Omics Visualizer 31 , that was used for visualization purposes in this work. Additionally, Cytoscape.js 32 was used to create interactive networks, available via a web interface at ( http://thalis.biol.uoa.gr/celegans_human_AD/ ), where detailed information about the proteins in the aforementioned networks can be retrieved.…”

Section: Methodsmentioning

confidence: 99%

Exploring the conservation of Alzheimer-related pathways between H. sapiens and C. elegans: a network alignment approach

Apostolakou

Sula

Nastou

et al. 2021

Sci Rep

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Alzheimer disease (AD) is a neurodegenerative disorder with an –as of yet– unclear etiology and pathogenesis. Research to unveil disease processes underlying AD often relies on the use of neurodegenerative disease model organisms, such as Caenorhabditis elegans. This study sought to identify biological pathways implicated in AD that are conserved in Homo sapiens and C. elegans. Protein–protein interaction networks were assembled for amyloid precursor protein (APP) and Tau in H. sapiens—two proteins whose aggregation is a hallmark in AD—and their orthologs APL-1 and PTL-1 for C. elegans. Global network alignment was used to compare these networks and determine similar, likely conserved, network regions. This comparison revealed that two prominent pathways, the APP-processing and the Tau-phosphorylation pathways, are highly conserved in both organisms. While the majority of interactions between proteins in those pathways are known to be associated with AD in human, they remain unexamined in C. elegans, signifying the need for their further investigation. In this work, we have highlighted conserved interactions related to AD in humans and have identified specific proteins that can act as targets for experimental studies in C. elegans, aiming to uncover the underlying mechanisms of AD.

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Section: Methodsmentioning

confidence: 99%

Exploring the conservation of Alzheimer-related pathways between H. sapiens and C. elegans: a network alignment approach

Apostolakou

Sula

Nastou

et al. 2021

Sci Rep

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“…All of the TF-genes were assembled into a gene regulatory network in glioma. The network was visualized by Cytoscape 3.6.1 30 , 31 .…”

Section: Methodsmentioning

confidence: 99%

Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma

Xiao¹,

Jin²,

Zhang³

et al. 2021

Theranostics

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Background: Enhancers are emerging regulatory regions controlling gene expression in diverse cancer types. However, the functions of enhancer regulatory circuit perturbations driven by copy number variations (CNVs) in malignant glioma are unclear. Therefore, we aimed to investigate the comprehensive enhancer regulatory perturbation and identify potential biomarkers in glioma. Results: We performed a meta-analysis of the enhancer centered regulatory circuit perturbations in 683 gliomas by integrating CNVs, gene expression, and transcription factors (TFs) binding. We found widespread CNVs of enhancers during glioma progression, and CNVs were associated with the perturbations of enhancer activities. In particular, the degree of perturbations for amplified enhancers was much greater accompanied by the glioma malignant progression. In addition, CNVs and enhancers cooperatively regulated the expressions of cancer-related genes. Genome-wide TF binding profiles revealed that enhancers were pervasively regulated by TFs. A network-based analysis of TF-enhancer-gene regulatory circuits revealed a core TF-gene module (58 interactions including seven genes and 14 TFs) that was associated survival of patients with glioma (p < 0.001). Finally, we validated this prognosis-associated TF-gene regulatory module in an independent cohort. In summary, our analyses provided new molecular insights for enhancer-centered transcriptional perturbation in glioma therapy. Conclusion: Integrative analysis revealed enhancer regulatory perturbations in glioma and also identified a network module that was associated with patient survival, thereby providing novel insights into enhancer-centered cancer therapy.

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“…Cytoscape: it is a type of open-source software used to analyze and visualize biological networks [ 26 ].…”

Section: Methodsmentioning

confidence: 99%

A Network Pharmacology to Explore the Mechanism of Astragalus Membranaceus in the Treatment of Diabetic Retinopathy

Jin

Hao

Xie

et al. 2020

Evidence-Based Complementary and Alternative Medicine

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Background. Diabetic retinopathy (DR) includes a series of typical lesions affected by retinal microvascular damage caused by diabetes mellitus (DM), which not only seriously damages the vision, affecting the life’s quality of patients, but also brings a considerable burden to the family and society. Astragalus Membranaceus (AM) is a commonly used medicine in clinical therapy of eye disorders in traditional Chinese medicine (TCM). In recent years, it is also used for treating DR, but the specific mechanism is unclear. Therefore, this study explores the potential mechanism of AM in DR treatment by using network pharmacology. Methods. Based on the oral bioavailability (OB) and drug likeness (DL) of two ADME (absorption, distribution, metabolism, excretion) parameters, Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), Swiss Target Prediction platform, GeneCards, and OMIM database were used to predict and screen the active compounds of AM, the core targets of AM in DR treatment. The Metascape data platform was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on the core targets. Results. 24 active compounds were obtained, such as quercetin, kaempferol, and astragaloside IV. There were 169 effective targets of AM in DR treatment, and the targets were further screened and finally, 38 core targets were obtained, such as VEGFA, AKT1, and IL-6. EGFR tyrosine kinase inhibitor resistance, AGE-RAGE signaling pathway in diabetic complications, PI3K-Akt signaling pathway, and other metabolic pathways participated in oxidative stress, cell apoptosis, angiogenesis signal transduction, inflammation, and other biological processes. Conclusion. AM treats DR through multiple compounds, multiple targets, and multiple pathways. AM may play a role in the treatment of DR by targeting VEGFA, AKT1, and IL-6 and participating in oxidative stress, angiogenesis, and inflammation.

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Visualize omics data on networks with Omics Visualizer, a Cytoscape App

Cited by 47 publications

References 11 publications

Exploring the conservation of Alzheimer-related pathways between H. sapiens and C. elegans: a network alignment approach

Exploring the conservation of Alzheimer-related pathways between H. sapiens and C. elegans: a network alignment approach

Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma

A Network Pharmacology to Explore the Mechanism of Astragalus Membranaceus in the Treatment of Diabetic Retinopathy

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