GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks

Camilo, Esther; Bovolenta, Luiz Augusto; Acencio, Márcio Luís; Castro, Mauro A. A.; Moreira, José Cláudio Fonseca; Lemke, Ney

doi:10.1093/bioinformatics/btt377

Cited by 5 publications

(2 citation statements)

References 7 publications

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“…Only genes with corrected p -values < 0.05 (FDR) were considered as differentially expressed ( Supplementary Table S2 ). Log-fold changes for each of the encoding genes of the proteins on the in silico model were exported from R into text files and plotted over the PPI network (metastatic vs. primary melanoma samples) by using the plugin GALANT for Cytoscape (Gaussian function sigma set to 0.04), which builds functional landscapes onto biological networks [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

Network-Based Identification of Altered Stem Cell Pluripotency and Calcium Signaling Pathways in Metastatic Melanoma

2018

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Malignancy of cancer has been linked to distinct subsets of stem-like cells, the so-called cancer stem cells (CSCs), which persist during treatment and seem to lead to drug-resistant recurrence. Metastatic spread of cancer cells is one of the hallmarks of malignancy and contributes to most human melanoma-related deaths. Recently, overlapping groups of proteins and pathways were shown to regulate stem cell migration and cancer metastasis, raising the question of whether genes/proteins involved in stem cell pluripotency may have important implications when applied to the biology of cancer metastasis. Furthermore, it is well known that ion channels and receptors, particularly those responsible for calcium (Ca2+) signal generation, are critical in determining the cellular fate of stem cells (SCs). In the present study, we searched for evidence of altered stem cell pluripotency and Ca2+ signaling-related genes in the context of melanoma metastasis. We did this by using network analysis of gene expression in tissue biopsies from three different independent datasets of patients. First, we created an in silico network model (“STEMCa” interactome) showing the landscape of interactions between stem cell pluripotency and Ca2+ signaling-related genes/proteins, and demonstrated that around 51% (151 out of 294) of the genes within this model displayed significant changes of expression (False Discovery Rate (FDR), corrected p-value < 0.05) in at least one of the datasets of melanoma metastasis when compared with primary tumor biopsies (controls). Analysis of the properties (degree and betweenness) of the topological network revealed 27 members as the most central hub (HB) and nonhub-bottlenecks (NH-B) among the 294 genes/proteins of the whole interactome. From those representative genes, CTNNB1, GNAQ, GSK3B, GSTP1, MAPK3, PPP1CC, PRKACA, and SMAD4 showed equal up- or downregulation (corrected p-value < 0.05) in at least 2 independent datasets of melanoma metastases samples and PTPN11 showed upregulation (corrected p-value < 0.05) in three of them when compared with control samples. We postulate that altered expression of stem cell pluripotency and Ca2+ signaling pathway-related genes may contribute to the metastatic transformation, with these central members being an optimal candidate group of biomarkers and in silico therapeutic targets for melanoma metastasis, which deserve further investigation.

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Section: Methodsmentioning

confidence: 99%

Network-Based Identification of Altered Stem Cell Pluripotency and Calcium Signaling Pathways in Metastatic Melanoma

2018

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“…For the network-level visualization of centrality values in the “BIOMARK” interactome, we utilized GALANT (GrAph LANdscape VisualizaTion). GALANT is a Cytoscape plugin that builds functional landscapes onto biological networks (Camilo et al, 2013 ). GALANT projects any kind of numerical data (e.g., centrality measurements) onto a network in order to create landscapes resembling the network layout, and also offers a friendly interface fully integrated with the Cytoscape where users can easily build their landscapes of interest by using one of the previously mentioned functions.…”

Section: Methodsmentioning

confidence: 99%

A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways

Zeidán-Chuliá

Gürsoy

Oliveira

et al. 2016

Front. Cell. Infect. Microbiol.

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Periodontitis, a formidable global health burden, is a common chronic disease that destroys tooth-supporting tissues. Biomarkers of the early phase of this progressive disease are of utmost importance for global health. In this context, saliva represents a non-invasive biosample. By using systems biology tools, we aimed to (1) identify an integrated interactome between matrix metalloproteinase (MMP)-REDOX/nitric oxide (NO) and apoptosis upstream pathways of periodontal inflammation, and (2) characterize the attendant topological network properties to uncover putative biomarkers to be tested in saliva from patients with periodontitis. Hence, we first generated a protein-protein network model of interactions (“BIOMARK” interactome) by using the STRING 10 database, a search tool for the retrieval of interacting genes/proteins, with “Experiments” and “Databases” as input options and a confidence score of 0.400. Second, we determined the centrality values (closeness, stress, degree or connectivity, and betweenness) for the “BIOMARK” members by using the Cytoscape software. We found Ubiquitin C (UBC), Jun proto-oncogene (JUN), and matrix metalloproteinase-14 (MMP14) as the most central hub- and non-hub-bottlenecks among the 211 genes/proteins of the whole interactome. We conclude that UBC, JUN, and MMP14 are likely an optimal candidate group of host-derived biomarkers, in combination with oral pathogenic bacteria-derived proteins, for detecting periodontitis at its early phase by using salivary samples from patients. These findings therefore have broader relevance for systems medicine in global health as well.

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Computational Approaches for Visualization and Integration of Omics Data

Sehgal

Moss

Ram

2014

Fundamentals of Advanced Omics Technologies: From Genes to Metabolites

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GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks

Abstract: http://www.lbbc.ibb.unesp.br/galant.

Cited by 5 publications

References 7 publications

Network-Based Identification of Altered Stem Cell Pluripotency and Calcium Signaling Pathways in Metastatic Melanoma

Network-Based Identification of Altered Stem Cell Pluripotency and Calcium Signaling Pathways in Metastatic Melanoma

A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways

Computational Approaches for Visualization and Integration of Omics Data

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