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--- worked_example3 [2016/02/09 10:08] – dcrespo
+++ worked_example3 [2017/05/24 15:27] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Worked example: ======
-===== Data and data source: =====
+===== Data and data source =====
-In this example we use {{:hcc4006_mutant_dmso.txt|gene expression data}} from NSCLC HCC4006 (EGFR<sub>m</sub>), downloaded from [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57156|GSE57156]].
+In this example we use gene expression data from NSCLC HCC4006 (EGFR<sub>m</sub>).
-====== Steps: ======
+The file can be downloaded from this link:
-  * Log in **PathAct**.
+{{:hcc4006_mutant_dmso.txt|hcc4006_mutant_dmso.txt}}
-  * Load example 2 by pressing //Load example file 2// button from the Expression matrix files panel. Once loaded, click on the //pathact_example_2.txt// button and load it.
+And was obtained from [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57156|GSE57156]] project.
-  * 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.
+===== Steps: =====
+  * 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 and launch a job with that file.
+{{ :ex3run.png?900 |}}
+  * A job will appear on the right and will be processed.
+{{ :ex3running.png?600 |}}
+  * Once finished, click on it to open the view window.
+ {{ :ex3ready.png?600 |}}
+  * The view window will appear.
+ {{ :view.png?800 |}}
+  * 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 |}}
@@ Line 15: / Line 47: @@
 **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).
@@ Line 59: / Line 91: @@
 **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).