worked_example_perturbation_effect
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worked_example_perturbation_effect [2019/08/08 15:51] krian created |
worked_example_perturbation_effect [2020/10/16 16:02] (current) krian |
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| * Log in Hipathia using login button on the top right corner, the login panel will appear. you can also login using an anonymous user. Please visit [[logging_in|Logging in]] in to further information on this step. | * Log in Hipathia using login button on the top right corner, the login panel will appear. you can also login using an anonymous user. Please visit [[logging_in|Logging in]] in to further information on this step. | ||
| {{ :loginhipathia.png |}} | {{ :loginhipathia.png |}} | ||
| - | * | + | * By clicking the Perturbation effect tool in the menu, the empty form will appear. |
| + | {{ :formeexampleperturbationeffect.png |}} | ||
| + | * Press the run example button, A study will appear on the My studies panel and will be processed. | ||
| + | {{ :run_example.png |}} | ||
| + | * Once finished, click on it to open the view window. | ||
| + | {{ :finishedexampleperturbationeffect.png |}} | ||
| + | * The view window will appear. | ||
| + | {{ :perturbationeffectexample1.png |}} | ||
| + | * Select the genes whose you want to modify its expression value. You can either click on a gene on the pathway viewer and change its value. | ||
| + | {{ :perturbationeffectexamplechangevalue1.png |}} | ||
| + | or search it in the Search genes… box of the Add genes panel. | ||
| + | {{ :drug.mp4?900 |}} | ||
| + | * You can modify the expression level of the genes listed in the Add genes panel and remove them from the list by pressing the **X** button to their right. The expression level of the removed genes will return to their original value. | ||
| + | |||
| + | For this example we fix the following expression values: | ||
| + | * IL6 | ||
| + | {{ :addgenesexample.png |}} | ||
| + | |||
| + | * Select the drugs targeting the objective genes if desired. We selected the "Siltuximab" drug for this example. | ||
| + | * Press the Update button from the Gene list panel.{{ :updatebtn.png |}} | ||
| + | The comparison is performed and the results prepared. | ||
| + | {{ :loadingperturbationeffectstudy.png |}} | ||
| + | * Visualize the results. For further information in the interpretation of the results, see [[Perturbation effect results|Perturbation effect results]]. | ||
worked_example_perturbation_effect.1565279476.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
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