Cytoscape: Software for Visualization and Analysis of Biological Networks

Köhl, Michael; Wiese, Sebastian; Warscheid, Bettina

doi:10.1007/978-1-60761-987-1_18

Cited by 1,169 publications

(911 citation statements)

References 30 publications

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“…G tests for independence were done to test whether samples are more connected within these categories than expected by chance. Visualization of the networks was performed in Cytoscape (Kohl et al, 2011) using the edge-weighted spring-embedded layout. Analysis of similarity (ANOSIM) calculations were performed to compare microbiome diversity across species and within species across time and location (Clarke, 1993;Chapman and Underwood, 1999).…”

Section: Dna Extraction and Preparationmentioning

confidence: 99%

Species specificity of symbiosis and secondary metabolism in ascidians

et al. 2014

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Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these 'chemical symbioses'. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R ¼ À 0.037, P-value ¼ 0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and biotechnological studies.

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Section: Dna Extraction and Preparationmentioning

confidence: 99%

Species specificity of symbiosis and secondary metabolism in ascidians

et al. 2014

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“…All interactions in STRING were provided with a probabilistic confidence score (combined score), and only interactions with combined score > 0.9 were retained in our analysis. Then the PPI network was constructed and visualized with the Cytoscape software [25].…”

Section: Methodsmentioning

confidence: 99%

RNA-Seq analysis for the potential targets and molecular mechanisms of 17 β-estradiol in squamous cell lung carcinoma

Chen¹,

Wü²,

Wang³

et al. 2016

neo

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The efficacy of 17 β-estradiol (E2) was valid in some cancers, while its effects on squamous cell lung carcinoma (SCLC) were still unclear. The aim of our study was to investigate the potential targets and molecular mechanisms of E2 in SCLC cells.Two RNA libraries from human lung carcinoma cells (SK-MES-1) with and without E2 treatment were constructed and sequenced. The differentially expressed genes (DEGs) between cells with or without E2 treatment were identified by cuffdiff software. Hierarchical Clustering Analysis (HCA) was performed for displaying gene expression changes and classification. Furthermore, enrichment analyses of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology Biological Process (GO BP) terms were performed through DAVID. The protein-protein interaction (PPI) network was constructed through STRING. Additionally, differentially expressed lncRNAs were also selected by cuffdiff software.Total 129 DEGs including 58 up-and 71 down-regulated genes were obtained. Cancer-related pathways including small cell lung cancer, hypertrophic cardiomyopathy (HCM) and pathways in cancer and biological processes including regulation of phosphorus metabolic process, protein localization and nucleus organization were enriched. The PPI network with 113 nodes and 312 edges was constructed. CASP3, ITGA2, COL4A6, PML and CDC25B were identified as hub nodes which had more interactions with others in the PPI network. Furthermore, eight up-regulated and ten down-regulated lncRNAs were selected.CASP3, ITGA2 and Lnc-DLK1-4:31 (one of down-regulated lncRNAs) might play pivotal roles in E2 treated SCNC cells by influencing cell apoptosis, angiogenesis and cell invasion respectively.Key words: squamous cell lung carcinoma, RNA-Seq, differentially expressed genes, lnc-RNA Squamous cell lung carcinoma (SCLC) is a common type of non-small-cell lung cancer (NSCLC) and the second leading cause of death related to lung cancer which causes approximately 400,000 deaths per year worldwide [1]. SCLC develops mainly in the upper airways and cigarette smokers are more susceptible to SCLC, therefore it is more common in men than in women [2]. Although various therapies such as radiation, chemotherapy, surgery and palliative care have been used for SCLC treatment, the overall therapeutic results were not optimistic [3,4]. A more thorough understanding of the mechanism of SCLC may offer a new hope on treatment innovations and prevention strategies.Estrogens are a group of human sex hormones which can be secreted primarily by the ovaries and placenta in women and the testes in men. The cell response to estrogens is in a concentration-dependent manner. Previous studies found that low concentration of 17 β-estradiol (E2) promoted the development of breast cancer and prostatic cancer, while 10 nM or higher concentration of E2 could cause cancer cell apoptosis [5][6][7]. The three major naturally occurring estrogens are E2, estrone and estriol, among them, E2 is the predominant and most active [8]. Meanwhile, Zhao et al...

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“…In our study, these differentially expressed cytokines were mapped into STRING database with combined score >0.5 for identifying the significant PPI pairs. PPI network was then established and visualized using Cytoscape software (Kohl, Wiese, & Warscheid, 2011). Degree centrality (Jeong, Mason, Barabási, & Oltvai, 2001) as a topological property of PPI network was then used to identify hub nodes in the network.…”

Section: Ppi Network Constructionmentioning

confidence: 99%

Protein microarray analysis identifies key cytokines associated with malignant middle cerebral artery infarction

Zhou

Zhang

et al. 2017

Brain and Behavior

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Introduction We aimed to explore potential cytokines involved in the malignant middle cerebral artery infarction ( MMI ) and elucidate their underlying regulatory mechanisms. Methods We first developed a cytokine profile by Quantibody ® Human Cytokine Antibody Array7000 using serum samples from eight patients with MMI and eight patients with non‐acute cerebral infarction ( NACI ). The differentially expressed cytokines were then identified in patients with MMI using two‐tailed Student's t ‐test and Fisher's Exact Test compared with patients with NACI . Gene Ontology and pathway enrichment analyses were performed using DAVID . Protein–protein interaction ( PPI ) network was constructed based on STRING database. Results A total of 10 differentially expressed cytokines were identified from 320 unique inflammatory cytokines in serums. Among them, four cytokines, like NCAM 1 (neural cell adhesion molecule 1), IGFBP ‐6 (insulin‐like growth factor binding protein 6), LYVE 1 (lymphatic vessel endothelial hyaluronan receptor 1), and LCN 2 (Lipocalin2), were up‐regulated, while another six cytokines, such as TGFB 1 (transforming growth factor, beta 1, also known as LAP ), EGF (epidermal growth factor), PDGFA (platelet‐derived growth factor alpha polypeptide), MMP ‐10 (matrix metallopeptidase 10), IL ‐27 (interleukin 27), and CCL 2 (chemokine (C‐C motif) receptor 2), were down‐regulated. Moreover, cytokine–cytokine receptor interaction pathway was significantly enriched. Conclusions Our findings indicate that 10 differentially expressed cytokines, such as NCAM 1, LCN 2, IGFBP‐6, LYVE1, MMP‐10, IL‐27, PDGFA , EGF , CCL 2, and TGFB 1 may participate in the development of MMI . Moreover, cytokine–cytokine receptor interaction pathway may be an important mechanism involved in this disease. These differentially expressed cytokines may serve as diagnostic biomarkers or drug targets for MMI .

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Cytoscape: Software for Visualization and Analysis of Biological Networks

Cited by 1,169 publications

References 30 publications

Species specificity of symbiosis and secondary metabolism in ascidians

Species specificity of symbiosis and secondary metabolism in ascidians

RNA-Seq analysis for the potential targets and molecular mechanisms of 17 β-estradiol in squamous cell lung carcinoma

Protein microarray analysis identifies key cytokines associated with malignant middle cerebral artery infarction

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