Help:PathwayStyling

From WikiPathways

Revision as of 23:34, 17 June 2016 (view source) Khanspers (Talk | contribs) (first draft) ← Previous diff		Current revision (21:47, 17 March 2023) (view source) Khanspers (Talk | contribs) (added titles to the last two)
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-	{|class="prettytable"	+	== 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 [http://www.cytoscape.org Cytoscape] can also be used to perform data-driven styling.
-	!WikiPathways	+
-	!Styled in Cytoscape	+	----
-	!Original publication figure	+	=== PDGFR-beta and ovarian cancer survival ===
-	|-	+	(Zhang, ''Cell'' 2016) [http://www.ncbi.nlm.nih.gov/pubmed/27372738 PubMed]
-	|[[Image:WP3645_85725.png|450px]]	+
-	|[[Image:NAD-biosynthetic-pathways_CS.png|450px]]	+
-	|[[Image:NAD_publication.png|500px]]	+	{|
		+	|[[Image:PDGFR-beta_pathway.png|border|500px|WikiPathways styled in Cytoscape]]
		+	|
		+	{|
		+	{{#imgLink:WP3972_92088.png|thumb|center |WikiPathways model|pathway|WP3972|WikiPathways model}}
		+	|-
		+	|[[Image:PDGFR-beta_original.png|thumb|Original figure]]
		+	|}
		+	|}
		+
		+	----
		+
		+	=== NAD⁺ in aging, metabolism, and neurodegeneration ===
		+	(Verdin, ''Science'' 2015) [http://www.ncbi.nlm.nih.gov/pubmed/26785480 PubMed]
		+
		+
		+	{|
		+	|[[Image:NAD-biosynthetic-pathways_CS.png|border|500px|WikiPathways styled in Cytoscape]]
		+	|
		+	{|
		+	{{#imgLink:WP3645_85725.png|thumb|center |WikiPathways model|pathway|WP3645|WikiPathways model}}
		+	|-
		+	|[[Image:NAD_publication.png|thumb|Original figure]]
		+	|}
		+	|}
		+
		+
		+
		+	----
		+	=== Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer ===
		+	(Yang, ''Mol Syst Biol'' 2014) [http://www.ncbi.nlm.nih.gov/pubmed/24799285 PubMed]
		+
		+	{|
		+	|[[Image:WP_Styling_Help_TCACycleCancer.png|600px|border|WikiPathways styled in Cytoscape]]
		+	|
		+	{|
		+	|{{#imgLink:WP2868_78079.png|thumb|center |WikiPathways model|pathway|WP2868|WikiPathways model}}
		+	|-
		+	|[[Image:TCACycleCancer_original.jpg|thumb|Original figure]]
		+	|}
		+	|}
		+
		+
		+	----
		+	=== Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease ===
		+	(Zhang et al, "Cell" 2013) [http://www.ncbi.nlm.nih.gov/pubmed/23622250 PubMed]
		+
		+	{|
		+	|[[Image:TYROBP_export.png|600px|border|WikiPathways styled in Cytoscape]]
		+	|
		+	{|
		+	|{{#imgLink:WP3625_85694.png|thumb|center|WikiPathways model|pathway|WP3625|WikiPathways model}}
		+	|-
		+	|[[Image:Tyrobp_original.png|thumb|Original figure]]
		+	|}
		+	|}
		+
		+
		+	----
		+	=== From systems to structure: bridging networks and mechanism ===
		+	(Fraser et al, "Mol. Cell." 2013) [http://www.ncbi.nlm.nih.gov/pubmed/23352243 PubMed]
		+
		+
		+	{|
		+	|[[Image:DualHijackModel_HIV.png|600px|border|WikiPathways styled in Cytoscape]]
		+	|
		+	{|
		+	|{{#imgLink:WP3300_85021.png|thumb|center|WikiPathways model|pathway|WP3300|WikiPathways model}}
		+	|-
		+	|[[Image:DualHijack_original.png‎|thumb|Original figure]]
		+	|}
	|}		|}

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Current revision

Contents 1 Styling WikiPathways Models 1.1 PDGFR-beta and ovarian cancer survival 1.2 NAD⁺ in aging, metabolism, and neurodegeneration 1.3 Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer 1.4 Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease 1.5 From systems to structure: bridging networks and mechanism

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.

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PDGFR-beta and ovarian cancer survival

(Zhang, Cell 2016) PubMed

WikiPathways model Original figure

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NAD⁺ in aging, metabolism, and neurodegeneration

(Verdin, Science 2015) PubMed

WikiPathways model Original figure

---

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

(Yang, Mol Syst Biol 2014) PubMed

WikiPathways model Original figure

---

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

(Zhang et al, "Cell" 2013) PubMed

WikiPathways model Original figure

---

From systems to structure: bridging networks and mechanism

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

WikiPathways model Original figure