Differences

This shows you the differences between two versions of the page.

--- pathway_viewer [2015/12/21 17:42] – created mhidalgo
+++ pathway_viewer [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 3: / Line 3: @@
 A pathway viewer has been develop in order to make easier the visualization of the comparison results.
-{{ :hipathia_viewer.png?600 |}}
+{{ :pathwayviewer1.png?800 |}}
 You can select the pathway to see in the //Pathways list// (**1**).
-You can also visualize a single subpath by clicking on its name (**3**) in the //Available subpaths// list (**2**). Subpaths depicted in blue are significantly down-regulated subpaths whereas those depicted in red are significantly up-regulated ones (p-value = 0.05). Subpaths depicted in grey are not significant.
+You can also visualize a single circuit by clicking on its name (**3**) in the //Available circuits// list (**2**). Circuits depicted in blue are significantly down-regulated circuits whereas those depicted in red are significantly up-regulated ones (p-value = 0.05). Circuits depicted in grey are not significant.
+===== Legend =====
-{{ :pretty_legend.png?600 |}}
+{{ ::metabolizer_legend.png?300 |}}
 The information summarized in the pathway viewer includes:
 Node's shape:
-  * **Ellipses** correspond to genes.
+  * **Rectangles** correspond to metabolic enzymatic.
   * **Circles** represent metabolites.
-  * **Rectangles** are cellular functions.
-Node's color (only when parameter //Color nodes by differential expression// has been selected):
+Node's color:
-  * **Blue** for down-regulated genes, **red** for up-regulated genes and **grey** for not significant genes.
+  * **Blue** for down-regulated reactions, **red** for up-regulated reactions and **grey** for not significant genes.
   * The intensity of the color depends on the significance of the differential expression.
-Edge's shape: Edges represent either activations or inhibitions.
+Edge's shape: Edges represent direction of the production by classic arrows.
-  * **Activations** are represented by classic arrows.
+  * Also gives information about reversible and irreversible reactions
-  * **Inhibitions** are represented by T arrows.
 Edge's color:
-  * Subpaths which are **up-regulated** in the disease condition have their arrows colored in **red**.
+  * Modules which are **up-regulated** in the disease condition have their arrows colored in **red**.
-  * Subpaths which are **down-regulated** in the disease condition have their arrows colored in **blue**.
+  * Modules which are **down-regulated** in the disease condition have their arrows colored in **blue**.
-  * Subpaths which are **not significative** for the test have their arrows colored in **grey**.
+  * Modules which are **not significant** for the test have their arrows colored in **grey**.
-  * When an edge belongs to different subpathways which should be colored in different colors, different arrows are depicted, each one for each necessary color.