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--- worked_example2 [2016/02/09 13:22] – fsalavert
+++ worked_example2 [2017/05/24 15:27] (current) – external edit 127.0.0.1
@@ Line 13: / Line 13: @@
 ===== Steps: =====
-  * Log in **PathAct** or use the start button to enter as anonymous.
+  * Log in **PathAct** using the login button on the top right corner, the login panel will appear.
 {{ :login.png?400 |}}
+  * You can also login as anonymous using the start button.
 {{ :start.png?400 |}}
-  * Upload the file as is shown in the [[Upload your data|Upload your data]] section.
+  * Upload the file as is shown in the [[Upload your data|Upload your data]] section and launch a job with that file.
-  * Load example 3 by pressing //Load example file 3// button from the Expression matrix files panel. Once loaded, click on the //pathact_example_3.txt// button and load it.
+{{ :ex2run.png?900 |}}
-  * In this example we simulate the effect of Tamoxifen __without__ using drug assistent. We add manually the targets ESR1 and  ESR2 (//Estrogen Receptor and Estrogen Receptor Beta//) to 0.1,  and PRKCA and EBP (//Protein kinase C// and //3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase//) to 0.4. //Figure 1// shows how modify the expression of those genes.
+  * A job will appear on the right and will be processed.
-{{ :screen_shot_2016-02-08_at_11.50.27_am.png?200 |}}
+{{ :ex2running.png?600 |}}
+  * Once finished, click on it to open the view window.
+ {{ :ex2ready.png?600 |}}
+  * The view window will appear.
+ {{ :view.png?800 |}}
+  * In this example we simulate the effect of Tamoxifen __without__ using drug assistent. We add manually the targets ESR1 and  ESR2 (//Estrogen Receptor and Estrogen Receptor Beta//) to 0.1,  and PRKCA and EBP (//Protein kinase C// and //3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase//) to 0.4. //Figure 1// shows how add and modify the expression of those genes.
+ {{ :ex2genesearch.png?400 |}}
+ {{ :ex2genelist.png?400 |}}
 **Figure 1:** Gene signal modification. Screenshot of gene selection panel. Note when we modify gene activity without drugs, no// Additional drug effect// appears.
-CellMaps visualizer highlights modified genes to help locate them (//figure 2//).
+The visualizer highlights modified genes to help locate them (//figure 2//).
-{{ :tg_gates_4.png?600 |}}
+{{ :ex2highlightnodes.png?800 |}}
-**Figure 2:** **A:** ErbB signaling pathway. **B:** Detail of ESR1 modification on the pathway. Note how CellMaps marks perturbed genes.
+**Figure 2:** **A:** Estrogen signaling pathway. Detail of ESR1 modification on the pathway. Note how the viewer marks perturbed genes.
   * Perform the inhibition by pressing update button. Those pathways and circuits that have been modified are marked in bold. Red or blue arrows indicate if those changes are or not significant (overactivated path or repressed).
@@ Line 51: / Line 69: @@
   * Finally, **PathAct** reports (//figure 5//) all the gene signal alterations and circuits log fold change, discriminating between significant or not (absolute FC > 2).