Help:PathwayStyling

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=== WikiPathways in Cytoscape ===
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== Styling WikiPathways Models ==
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The recommended default style of WikiPathways is optimized for clarity, data overlay and analysis, and therefor sometimes lacks the rich visual qualities of pathway figures in publications. However, because of it's flexibility, the WikiPathways format can be used in a number of analysis and visualization tools, where the content can be customized for specific purposes. Here we demonstrate how WikiPathways can be customized for creating publication-quality figures, by styling the pathways in Cytoscape. The pathways represented were created based on existing published figures. For each pathway, thumbnails for the original publication figure and the WikiPathways model are included as thumbnails.
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A showcase of WikiPathways models styled to produce images comparable to original static figures. You can model and then style any biological process, starting from a published figure or your own research results. Visualization tools like [http://www.cytoscape.org Cytoscape] can also be used to perform data-driven styling.  
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=== PDGFR-beta and ovarian cancer survival ===
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(Zhang, ''Cell'' 2016) [http://www.ncbi.nlm.nih.gov/pubmed/27372738 PubMed]
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{|
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|[[Image:PDGFR-beta_pathway.png|border|500px|WikiPathways styled in Cytoscape]]
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{|
{|
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|[[Image:NAD-biosynthetic-pathways_CS.png|500px|border]]
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{{#imgLink:WP3972_92088.png|thumb|center |WikiPathways model|pathway|WP3972|WikiPathways model}}
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|[[Image:PDGFR-beta_original.png|thumb|Original figure]]
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|}
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|}
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=== NAD⁺ in aging, metabolism, and neurodegeneration ===
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(Verdin, ''Science'' 2015) [http://www.ncbi.nlm.nih.gov/pubmed/26785480 PubMed]
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{|
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|[[Image:NAD-biosynthetic-pathways_CS.png|border|500px|WikiPathways styled in Cytoscape]]
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{|
{|
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|[[Image:WP3645_85725.png|thumb|WikiPathways]]
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{{#imgLink:WP3645_85725.png|thumb|center |WikiPathways model|pathway|WP3645|WikiPathways model}}
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|[[Image:NAD_publication.png|thumb|Original]]
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|[[Image:NAD_publication.png|thumb|Original figure]]
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|}
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|}
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=== Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer ===
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(Yang, ''Mol Syst Biol'' 2014) [http://www.ncbi.nlm.nih.gov/pubmed/24799285 PubMed]
{|
{|
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  |[[Image:WP_Styling_Help_TCACycleCancer.png|600px|border]]
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  |[[Image:WP_Styling_Help_TCACycleCancer.png|600px|border|WikiPathways styled in Cytoscape]]
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{|
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|{{#imgLink:WP2868_78079.png|thumb|center |WikiPathways model|pathway|WP2868|WikiPathways model}}
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|-
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|[[Image:TCACycleCancer_original.jpg|thumb|Original figure]]
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|}
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|}
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=== Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease ===
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(Zhang et al, "Cell" 2013) [http://www.ncbi.nlm.nih.gov/pubmed/23622250 PubMed]
{|
{|
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|[[Image:WP2868_78079.png|thumb|WikiPathways]]
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|[[Image:TYROBP_export.png|600px|border|WikiPathways styled in Cytoscape]]
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|[[Image:TCACycleCancer_original.jpg|thumb|Original]]
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{|
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|{{#imgLink:WP3625_85694.png|thumb|center|WikiPathways model|pathway|WP3625|WikiPathways model}}
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|[[Image:Tyrobp_original.png|thumb|Original figure]]
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|}
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|}
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=== From systems to structure: bridging networks and mechanism ===
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(Fraser et al, "Mol. Cell." 2013) [http://www.ncbi.nlm.nih.gov/pubmed/23352243 PubMed]
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{|
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|[[Image:DualHijackModel_HIV.png|600px|border|WikiPathways styled in Cytoscape]]
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{|
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|{{#imgLink:WP3300_85021.png|thumb|center|WikiPathways model|pathway|WP3300|WikiPathways model}}
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|-
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|[[Image:DualHijack_original.png‎|thumb|Original figure]]
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Current revision

Contents

Styling WikiPathways Models

A showcase of WikiPathways models styled to produce images comparable to original static figures. You can model and then style any biological process, starting from a published figure or your own research results. Visualization tools like Cytoscape can also be used to perform data-driven styling.

PDGFR-beta and ovarian cancer survival

(Zhang, Cell 2016) PubMed


WikiPathways styled in Cytoscape
Original figure
Original figure

NAD⁺ in aging, metabolism, and neurodegeneration

(Verdin, Science 2015) PubMed


WikiPathways styled in Cytoscape
Original figure
Original figure


Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer

(Yang, Mol Syst Biol 2014) PubMed

WikiPathways styled in Cytoscape
Original figure
Original figure


Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease

(Zhang et al, "Cell" 2013) PubMed

WikiPathways styled in Cytoscape
Original figure
Original figure


From systems to structure: bridging networks and mechanism

(Fraser et al, "Mol. Cell." 2013) PubMed


WikiPathways styled in Cytoscape
Original figure
Original figure
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