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worked_example2 [2016/02/09 13:47] – fsalavertworked_example2 [2017/05/24 15:27] (current) – external edit 127.0.0.1
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 ===== Steps: ===== ===== Steps: =====
  
-  * Log in **PathAct** using the login button on the top right corner.+  * Log in **PathAct** using the login button on the top right corner, the login panel will appear.
  
 {{ :login.png?400 |}} {{ :login.png?400 |}}
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   * Upload the file as is shown in the [[Upload your data|Upload your data]] section and launch a job with that file.    * Upload the file as is shown in the [[Upload your data|Upload your data]] section and launch a job with that file. 
  
-{{ :ex2run.png?600 |}}+{{ :ex2run.png?900 |}}
  
   * A job will appear on the right and will be processed.   * A job will appear on the right and will be processed.
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  {{ :ex2ready.png?600 |}}  {{ :ex2ready.png?600 |}}
  
-  * 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. +  * The view window will appear.
  
-  * 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.+ {{ :view.png?800 |}}
  
-{{ :screen_shot_2016-02-08_at_11.50.27_am.png?200 |}}+ 
 +  * 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. 
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 + {{ :ex2genesearch.png?400 |}} 
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 + {{ :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. **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).   * 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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   * Finally, **PathAct** reports (//figure 5//) all the gene signal alterations and circuits log fold change, discriminating between significant or not (absolute FC > 2).   * Finally, **PathAct** reports (//figure 5//) all the gene signal alterations and circuits log fold change, discriminating between significant or not (absolute FC > 2).
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worked_example2.1455025678.txt.gz · Last modified: 2017/05/24 15:27 (external edit)