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in-silico_knockout:over_expression [2016/12/26 12:19] – 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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 {{ :in-silico_knockout:metabolizer_ko_1_2.png?600 |}} {{ :in-silico_knockout:metabolizer_ko_1_2.png?600 |}}
  
-1-2) This section shows the input data and parameters that you used for current job.+**1-2)** This section shows the input data and parameters that you used for current job.
 Missing genes are the genes which are not contained by the expression data you provided. Missing genes are the genes which are not contained by the expression data you provided.
 Therefore user may not use them for knockout or over expression. Therefore user may not use them for knockout or over expression.
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 {{ :in-silico_knockout:metabolizer_ko_3_4.png?600 |}} {{ :in-silico_knockout:metabolizer_ko_3_4.png?600 |}}
  
-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.
 Table contains class probability of selected sample before knockout and after knockout. Table contains class probability of selected sample before knockout and after knockout.
 On this table you can find results for manipulation of all metabolic module genes. On this table you can find results for manipulation of all metabolic module genes.
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-5) The interactive pathway viewer lets user to see the results in network structure.+**5)** The interactive pathway viewer lets user to see the results in network structure.
 Please check the color and shape codings of pathway viewer. Please check the color and shape codings of pathway viewer.
 You can right click on nodes to get detailed information about them. Left click will You can right click on nodes to get detailed information about them. Left click will
 show you the expression value of the gene(s)which involved with the selected reaction. show you the expression value of the gene(s)which involved with the selected reaction.
-You can modify the expression value from these window (7). +You can modify the expression value from these window **(7)**.
  
-6) If you have list of genes which you want to knockout. You can search them and update their expression values on add genes panel +**6)** If you have list of genes which you want to knockout. You can search them and update their expression values on add genes panel 
-If selected genes targeted by any drug or chemical, they will shown on "selected gene related drugs panel" (8).+If selected genes targeted by any drug or chemical, they will shown on "selected gene related drugs panel" **(8)**.
 User can choose any of these drugs to knockout/overexpress the genes.  User can choose any of these drugs to knockout/overexpress the genes. 
  
-9) If you have a list of drugs which you want to know their effects on activity of metabolic modules.+**9)** If you have a list of drugs which you want to know their effects on activity of metabolic modules.
 You can search drugs on "add drugs" panel. Genes which are targeted by drug you selected on add drugs panel will be shown on genes affected by drugs panel (10). You can search drugs on "add drugs" panel. Genes which are targeted by drug you selected on add drugs panel will be shown on genes affected by drugs panel (10).
  
  
-11) You can search and navigate between metabolic networks using Pathways section.+**11)** You can search and navigate between metabolic networks using Pathways section.
 tide the selected metabolic pathway. In this section you can select module and highlight it to see tide the selected metabolic pathway. In this section you can select module and highlight it to see
 enire module structure. enire module structure.
  
  
-13) Once you set all knockout/overexpresion rules, you can click on update button to calculate the effect of the gene expresion manuplations.+**13)** Once you set all knockout/overexpresion rules, you can click on update button to calculate the effect of the gene expresion manuplations.
  
-14) If you want to return initial results and do new knockout/overexpression +**14)** If you want to return initial results and do new knockout/overexpression 
 combinations. You can click on clear button.sdcasd combinations. You can click on clear button.sdcasd
  
 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:metabolizer_ko_15.png?300 |}}+{{ :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_knockout:metabolizer_ko_16.png?300 |}}+{{ :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.
 Under this table you can find class probabilty of sample for before and after Under this table you can find class probabilty of sample for before and after
 gene expreesion mauolatin gene expreesion mauolatin
in-silico_knockout/over_expression.1482754782.txt.gz · Last modified: 2017/05/24 14:33 (external edit)