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--- worked_example3 [2016/02/09 14:40] – fsalavert
+++ worked_example3 [2017/05/24 15:27] (current) – external edit 127.0.0.1
@@ Line 37: / Line 37: @@
-  * In this example we simulate the effect of treating cells with Erlotinib (FDA approved EGFR inhibitor for treatment of NSCLC EGFR mutant). We modify the target actions fixing: Agonist = 0.8 and Antagonist = 0.1 (mechanisms of action of Erlotinib on its targets).// Figure 1// shows how modify the expression of those genes.
+  * In this example we simulate the effect of treating cells with Erlotinib (FDA approved EGFR inhibitor for treatment of NSCLC EGFR mutant). We modify the target actions fixing: Agonist = 0.8 and Antagonist = 0.1 (mechanisms of action of Erlotinib on its targets).// Figure 1// shows how modify the expression of those genes using the setting panel.
+  *  To open the settings panel click on the //Settings// button located at the top right corner.
+ {{ :ex3settings.png?400 |}}
 {{ :gse57156_3.png?600 |}}
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 **Figure 1:** Gene signal modification. **A:** Screenshot of gene selection panel. Note how the drug list appears when we select any gene. **B:** We modify the effect of drug action on its targets (in our case, agonist and antagonist, mark with red arrow and stars).** C:** Screenshot of gene selection panel after In Silico treatment with erlotinib. We have had to manually modify the expression of “EGFR - EGFR node” and “GRB2 EGFR node” because the drug annotations doesn't contain those targets.
-CellMaps visualizer highlights modified genes to help locate them (//figure 2//).
+The visualizer highlights modified genes to help locate them (//figure 2//).
 {{ :gse57156_4.png?600 |}}
-**Figure 2: A:** ErbB signaling pathway. **B:** Detail of EGFR modification on the pathway. Note how CellMaps marks perturbed genes.
+**Figure 2: A:** ErbB signaling pathway. **B:** Detail of EGFR modification on the pathway. Note how the visualizer 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).
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 **Figure 9:** PathAct report. **A:** list of perturbed genes and final value of activation. **B:** ranked circuits by log fold change (base 10). Note how PTEN logFC are -Infinite (PTEN loss represents a complete depletion of PTEN - complete node inactivation). **C:** Fold change is used by calculate significance using 2 as threshold (log<sub>e</sub>2 = 0.6931472).