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in-silico_knockout:over_expression [2016/12/26 12:21] – ccubukin-silico_knockout:over_expression [2017/05/24 14:33] (current) – external edit 127.0.0.1
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 =====  In-silico knockout and over expression ===== =====  In-silico knockout and over expression =====
  
-Metabolizer allows you to simulate knockout (KO) and/or over-expression (OE) of one or several genes or the effect of a drug in metabolic module genes.+Metabolizer allows you to simulate effect of knockout (KO) and/or over-expression (OE) of one or several genes or the effect of drug(s) in the activity of metabolic modules.
  
 2 different usage of Knockout tool exist: 2 different usage of Knockout tool exist:
 +
 +
 +The tool can be accessed from the main menu bar, by clicking on the //Knockout// button, see [[workflow KO|Workflow]] for further information.
 +
 +The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels:
 +
 +Once the form has been filled in, press the //Launch job// button to launch a job. Your job will be listed in the //My jobs// panel, see [[workflow|Workflow]] for further information.
 +
  
 **1) Using sample** \\ **1) Using sample** \\
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 **2) Using a dataset (Multiple Samples)** \\ **2) Using a dataset (Multiple Samples)** \\
  
-The tool can be accessed from the main menu bar, by clicking on the //Knockout// button, see [[workflow KO|Workflow]] for further information. 
  
-The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels: 
   * [[http://metabolizer.babelomics.org/doc/doku.php?id=input_data|Input data]]   * [[http://metabolizer.babelomics.org/doc/doku.php?id=input_data|Input data]]
   * [[Design data|Design data]]   * [[Design data|Design data]]
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   * [[http://metabolizer.babelomics.org/doc/doku.php?id=job_information|Job information]]   * [[http://metabolizer.babelomics.org/doc/doku.php?id=job_information|Job information]]
  
-Once the form has been filled in, press the //Launch job// button to launch a job. Your job will be listed in the //My jobs// panel, see [[workflow|Workflow]] for further information. 
  
 === OUTPUT === === OUTPUT ===
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 **3)** An informative plot for the normalized (between 0 and 1) gene expression values.  **3)** An informative plot for the normalized (between 0 and 1) gene expression values. 
  
-{{ :in-silico_knockout:metabolizer_interactive_page.png?300 |}}+{{ :in-silico_knockout:metabolizer_interactive_page.png?600 |}}
  
 **4)** Class probability table shows results of the auto knockout. **4)** Class probability table shows results of the auto knockout.
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 When update process finishes you will see your results on the same page. When update process finishes you will see your results on the same page.
  
-{{ :in-silico_knockout:me3abolizer_ko_15.png?600 |}}+{{ :in-silico_knockout:metabolizer_ko_15.png?600 |}}
  
 **15)** This table shows which genes you knockout/overexpressed, type of the knockout and weigth **15)** This table shows which genes you knockout/overexpressed, type of the knockout and weigth
 of the manuplation. of the manuplation.
  
-{{ :in-silico_knockou3:metabolizer_ko_16.png?600 |}}+{{ :in-silico_knockout:metabolizer_ko_16.png?600 |}}
  
 **16)** Module impact table shows which modules and how they are affected from gene expression manipulations. **16)** Module impact table shows which modules and how they are affected from gene expression manipulations.
in-silico_knockout/over_expression.1482754904.txt.gz · Last modified: 2017/05/24 14:33 (external edit)