VISIBIOweb: visualization and layout services for BioPAX pathway models

Dilek, Alptug; Belviranlı, Mehmet E.; Doğrusöz, Uğur

doi:10.1093/nar/gkq352

Cited by 14 publications

(14 citation statements)

References 16 publications

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“…GPML format can be used for pathway enrichment analysis using GeneSpring (Agilent). The CCR7 signaling data provided in these formats may also be visualized and analysed using the software such as Cytoscape ( 33 ), GenMAPP, Visualization and layout services for BioPAX pathway models (VISIBIOweb) ( 34 ) and Chisio BioPAX Editor (ChiBE) ( 35 ). The pathway data will be updated periodically as more reactions become available.…”

Section: Development Of a Cell-type-specific Differential-ligand Signmentioning

confidence: 99%

Differential ligand-signaling network of CCL19/CCL21-CCR7 system

et al. 2015

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Chemokine (C-C motif) receptor 7 (CCR7), a class A subtype G-Protein Coupled Receptor (GPCR), is involved in the migration, activation and survival of multiple cell types including dendritic cells, T cells, eosinophils, B cells, endothelial cells and different cancer cells. Together, CCR7 signaling system has been implicated in diverse biological processes such as lymph node homeostasis, T cell activation, immune tolerance, inflammatory response and cancer metastasis. CCL19 and CCL21, the two well-characterized CCR7 ligands, have been established to be differential in their signaling through CCR7 in multiple cell types. Although the differential ligand signaling through single receptor have been suggested for many receptors including GPCRs, there exists no resource or platform to analyse them globally. Here, first of its kind, we present the cell-type-specific differential signaling network of CCL19/CCL21-CCR7 system for effective visualization and differential analysis of chemokine/GPCR signaling.Database URL: http:// www. netpath. org/ pathways? path_ id= NetPath_ 46.

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Section: Development Of a Cell-type-specific Differential-ligand Signmentioning

confidence: 99%

Differential ligand-signaling network of CCL19/CCL21-CCR7 system

et al. 2015

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“…The pathway reactions are encoded in various community standard data exchange formats such as Proteomics Standards Initiative for Molecular Interaction (PSI-MI version 2.5) ( 47 ), Biological PAthway eXchange (BioPAX level 3) ( 48 ) and Systems Biology Markup Language (SBML version 2.1) ( 49 ). Users can download these files from NetPath and import them in various freely available software such as Cytoscape ( 50 ), VISIBIOweb ( 51 ) and ChiBE ( 52 ) to visualize the pathway reactions. The data are also available in tab delimited and Microsoft Excel formats.…”

Section: Data Formats Availability and Visualizationmentioning

confidence: 99%

TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling

et al. 2014

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Thymic stromal lymphopoietin (TSLP) is a four-helix bundle cytokine that plays a critical role in the regulation of immune responses and in the differentiation of hematopoietic cells. TSLP signals through a heterodimeric receptor complex consisting of an interleukin-7 receptor α chain and a unique TSLP receptor (TSLPR) [also known as cytokine receptor-like factor 2 (CRLF2)]. Cellular targets of TSLP include dendritic cells, B cells, mast cells, regulatory T (Treg) cells and CD4+ and CD8+ T cells. The TSLP/TSLPR axis can activate multiple signaling transduction pathways including the JAK/STAT pathway and the PI-3 kinase pathway. Aberrant TSLP/TSLPR signaling has been associated with a variety of human diseases including asthma, atopic dermatitis, nasal polyposis, inflammatory bowel disease, eosinophilic eosophagitis and, most recently, acute lymphoblastic leukemia. A centralized resource of the TSLP signaling pathway cataloging signaling events is not yet available. In this study, we present a literature-annotated resource of reactions in the TSLP signaling pathway. This pathway map is publicly available through NetPath (http://www.netpath.org/), an open access signal transduction pathway resource developed previously by our group. This map includes 236 molecules and 252 reactions that are involved in TSLP/TSLPR signaling pathway. We expect that the TSLP signaling pathway map will provide a rich resource to study the biology of this important cytokine as well as to identify novel therapeutic targets for diseases associated with dysregulated TSLP/TSLPR signaling.Database URL: http://www.netpath.org/pathways?path_id=NetPath_24

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“…Users can download these files from the database to visualize modifications are also mentioned, wherever available. Upon stimulation of IL-17, important signaling pathways including PI3K-AKT, Ras-MAPK, and NFκB are found to be activated the pathway reactions using various freely available software such as Cytoscape (Shannon et al 2003) and VISIBIOweb (Dilek et al 2010). The data is also accessible in tab delimited and Microsoft Excel formats.…”

Section: Resultsmentioning

confidence: 99%

A knowledgebase resource for interleukin-17 family mediated signaling

Sharma

Balakrishnan

Datta

et al. 2015

J. Cell Commun. Signal.

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Interleukin-17 (IL-17) belongs to a relatively new family of cytokines that has garnered attention as the signature cytokine of Th17 cells. This cytokine family consists of 6 ligands, which bind to 5 receptor subtypes and induce downstream signaling. Although the receptors are ubiquitously expressed, cellular responses to ligands vary across tissues. The cytokine family is associated with various autoimmune disorders including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, asthma and psoriasis in addition to being implicated in the pathogenesis of cancer. In addition, this family plays a role in host defense against bacterial and fungal infections. The signaling mechanisms of the IL-17 family of proinflammatory cytokines are not well explored. In this study, we present a resource of literature-annotated reactions induced by IL-17. The reactions are catalogued under 5 categories, namely; molecular association, catalysis, transport, activation/inhibition and gene regulation. A total of 93 molecules and 122 reactions have been annotated. The IL-17 pathway is freely available through NetPath, a resource of signal transduction pathways previously developed by our group.

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VISIBIOweb: visualization and layout services for BioPAX pathway models

Cited by 14 publications

References 16 publications

Differential ligand-signaling network of CCL19/CCL21-CCR7 system

Differential ligand-signaling network of CCL19/CCL21-CCR7 system

TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling

A knowledgebase resource for interleukin-17 family mediated signaling

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