Biological network analysis with CentiScaPe: centralities and experimental dataset integration

Scardoni, Giovanni; Tosadori, Gabriele; Faizan, Mohammed; Spoto, Fausto; Fabbri, F.; Laudanna, Carlo

doi:10.12688/f1000research.4477.2

Cited by 91 publications

(58 citation statements)

References 20 publications

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“…Cytoscape plugin BisoGenet was applied to visualize the genes' interactions (Martin et al, 2010). The topology of the network was carried out by the CentiScaPe v2.2 (Scardoni et al, 2014). The…”

Section: Network Visualizationmentioning

confidence: 99%

miR‐298 plays a pivotal role in colon cancer invasiveness by targeting PTEN

Arabsorkhi

Gharib

Khojini

et al. 2019

Journal Cellular Physiology

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Evidence indicate that the miR-298 dysregulation might associate with colorectal cancer (CRC) development. Herein, we evaluated the effect of miR-298 dysregulation on colon cancer invasiveness. First, metabolic activity, cell cycle progression, apoptosis, and invasion of miR-298 overexpressed/knocked out colon cancer cells were examined and combined with their transcriptome analysis data for better visualization of miR-298 intracellular signaling networks. Interaction between miR-298 and its target was evaluated with luciferase assay and validated using western blot analysis. The proportion of abnormal miR-298 level was investigated in tumor samples, matched normal adjacent tissues, and plasmas of 100 CRC patients, and also compared with 100 normal plasma samples. TheMann-Whitney U test was performed to assess miR-298 differences among the studied groups, and the correlation between miR-298 and the risk of CRC was shown by univariate and multivariate logistic regression. The data indicate that miR-298 overexpression promoted proliferation and metastasis in CRC cells via targeting phosphatase and tensin homolog. Comparative analysis of CRC tumors, normal adjacent tissues, and plasmas indicated a significant miR-298 upregulation in tumors and plasmas (1.72-fold and 1.65fold, respectively; p < .001). Also, the aberrant level of miR-298 contributed with CRC tumor differentiation, TNM stage and lymph node metastasis (p < .001), and independently associated with poor survival of CRC patients (p < .029; hazard ratio: 1.292; 95% confidence interval: 0.339-2.184). Collectively, these data showed that abnormal level of miR-298 correlated with cancer development and through that lowered the overall survival rate of CRC patients. Therefore, miR-298 could be considered as a therapeutic target for CRC. K E Y W O R D S colorectal cancer, invasion, metastasis, microRNA-298, PTEN

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Section: Network Visualizationmentioning

confidence: 99%

miR‐298 plays a pivotal role in colon cancer invasiveness by targeting PTEN

Arabsorkhi

Gharib

Khojini

et al. 2019

Journal Cellular Physiology

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“…Genes interactions were estimated with the Cytoscape plugin BisoGenet (Martin et al, 2010). The CentiScaPe version 2.2 was applied for network topology (Scardoni et al, 2014). The DEGs were annotated using the Enrichr algorithms (http://amp.pharm.mssm.edu/Enrichr/).…”

Section: Methodsmentioning

confidence: 99%

miR‐497‐5p mediates starvation‐induced death in colon cancer cells by targeting acyl‐CoA synthetase‐5 and modulation of lipid metabolism

Gharib

Nasrabadi

Zali

2020

Journal Cellular Physiology

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Modulation of fatty acids metabolism is an appropriate strategy for starvation‐induced death in tumor cancers. Colon cancer cells express a high level of acyl‐CoA synthetase‐5 (ACSL5), and as yet no therapeutic approach has been achieved. Herein, ACSL5‐related microRNAs (miRNAs) were identified via TargetScan, and their impacts on ACSL5 and lipid content along with metabolic activity, cell cycle, migration, and invasion of colorectal cancer (CRC) cells were examined, and subsequently compared with transcriptome for better visualization of intracellular‐signaling networks. In vivo analysis was performed using BALB/c mice xenograft model of CRC injected with target miRNA. Clinical significances were also evaluated in 80 CRC tumors and matched adjacent normal tissues. There was a reverse correlation between ACSL5 and miR‐497‐5p, which miR‐497‐5p overexpression modulated CRC cell proliferation and development. A similar observation was received from the in vivo examination in which intratumoral injection of miR‐497‐5p reversed the tumor growth in the CRC xenograft model. Downregulation of miR‐497‐5p correlated with tumor differentiation, tumor, node, and metastasis staging, lymph node metastasis, and poor survival in patients with CRC. These results suggested that miR‐497‐5p upregulation could be considered as a therapeutic strategy for modulation of lipid metabolism in colon cancer.

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“…The PPI network was shown in Cytoscape (Version 3.6.1, Cytoscape Consortium, U.S) and the unconnected nodes were discarded, which had 952 nodes and 4824 edges. Centiscape [15], the app of Cytoscape, was used to calculate the degree measure of each node. Referring to the previous study of others [16,17], we determined the nodes whose degree were more than twice the mean degree value as hub genes.…”

Section: The Construction and Analyzing Of Ppi Networkmentioning

confidence: 99%

Discovery of potential drugs for COVID-19 based on the connectivity map

Li¹,

Bai²,

Yang³

et al. 2020

Preprint

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Background: Corona virus infective disease 19 is the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and spreads very rapidly, which become a worldwide public healthy crisis. Until now, there is no effective antivirus drugs or vaccines specifically used for its treatment. So it is urgent to discover efficient therapeutic methods. The same as SARS-CoV, SARS-CoV-2 also invades organism by combining with Angiotensin-converting enzyme 2 (ACE2). Recently, there are reports about SARS-CoV-2 infected host not only through the respiratory tract, but also gastrointestinal tract. However, it is proved that ACE2 plays a key role in protecting subjects from lung injury and resisting the inflammation caused by intestinal epithelial damage. Interestingly, the expression of ACE2 protein is reduced after SARS-CoV infection.Methods: According to the dataset of genes co-expressed with ACE2 in the colonic epithelial cells, we established a protein-protein interaction (PPI) Network and selected hub genes from them. The cluster analysis was performed to find out the dense region of the PPI Network. Then, gene ontology (GO) and pathway enrichment analysis were performed to explore the main function of genes co-expressed with ACE2. Finally, we predicted the potential drugs for the treatment of COVID-19 based on the connectivity map (Cmap) .Results: We constructed a PPI network containing 125 hub genes of genes co-expressed with ACE2 in the colonic epithelial cells and obtained two modules through cluster analysis. The GO analysis and the KEGG pathway revealed these genes were aggregated in ribosome, exosomes, extracellular cellular components; structure constituent of ribosome, G-protein coupled receptor activity, MHC class I and II receptor activity biological processes; immune response, protein metabolism, signal transduction biological processes; and ribosome, graft-versus-host disease, viral myocarditis pathways. The result

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Biological network analysis with CentiScaPe: centralities and experimental dataset integration

Cited by 91 publications

References 20 publications

miR‐298 plays a pivotal role in colon cancer invasiveness by targeting PTEN

miR‐298 plays a pivotal role in colon cancer invasiveness by targeting PTEN

miR‐497‐5p mediates starvation‐induced death in colon cancer cells by targeting acyl‐CoA synthetase‐5 and modulation of lipid metabolism

Discovery of potential drugs for COVID-19 based on the connectivity map

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