Help:PathwayStyling

From WikiPathways

Revision as of 18:56, 28 June 2016 (view source) Khanspers (Talk | contribs) ← Previous diff		Current revision (21:47, 17 March 2023) (view source) Khanspers (Talk | contribs) (added titles to the last two)
(11 intermediate revisions not shown.)
Line 1:		Line 1:
-	=== WikiPathways in Cytoscape ===	+	== Styling WikiPathways Models ==
-	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.	+	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.
		+	----
		+	=== PDGFR-beta and ovarian cancer survival ===
		+	(Zhang, ''Cell'' 2016) [http://www.ncbi.nlm.nih.gov/pubmed/27372738 PubMed]
		+
		+
		+	{|
		+	|[[Image:PDGFR-beta_pathway.png|border|500px|WikiPathways styled in Cytoscape]]
		+	|
	{|		{|
-	|[[Image:NAD-biosynthetic-pathways_CS.png|500px|border]]	+	{{#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]]
		+	|
	{|		{|
-	|[[Image:WP3645_85725.png|thumb|WikiPathways]]	+	{{#imgLink:WP3645_85725.png|thumb|center |WikiPathways model|pathway|WP3645|WikiPathways model}}
-	|[[Image:NAD_publication.png|thumb|Original]]	+	|-
		+	|[[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]]	+	|[[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:WP2868_78079.png|thumb|WikiPathways]]	+	|[[Image:TYROBP_export.png|600px|border|WikiPathways styled in Cytoscape]]
-	|[[Image:TCACycleCancer_original.jpg|thumb|Original]]	+	|
		+	{|
		+	|{{#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]]
		+	|}
	|}		|}

---

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.

---

PDGFR-beta and ovarian cancer survival

(Zhang, Cell 2016) PubMed

WikiPathways model Original figure

---

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