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snow [2010/05/31 12:53]
jsantoyo
snow [2010/05/31 13:00] (current)
jsantoyo
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 The following sections are the recipes to follow according to the data you have and depending on what type of analysis you want to perform. The following sections are the recipes to follow according to the data you have and depending on what type of analysis you want to perform.
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 ==== 1. One list analysis ==== ==== 1. One list analysis ====
 **1.1. Scenario:​** ​ You have a list of proteins or genes that you have selected for a particular reason, for instance they are the result of a differential expression analysis of a microarray experiment, they are the spots identiyied as differentiate two samples in a two-dimensional gel electrophoresis or they have an interesting pattern of expression along several samples in a trancriptomic analysis. From this list of proteins/​genes you want to find out whether they have something in common in terms of functionality. The lits have been selected under some particular reason that a priori may suggest that they migth be functionaly related. There are several programs/​tools that try to extract those functionalities that are behind the set of genes/​proteins,​ FatiGO or Marmite are two examples (find them within Babelomics. SNOW is another program with this aim, its particularity is that it uses protein-protein interaction data and evaluates protein/​gene modules with a structural component. **1.1. Scenario:​** ​ You have a list of proteins or genes that you have selected for a particular reason, for instance they are the result of a differential expression analysis of a microarray experiment, they are the spots identiyied as differentiate two samples in a two-dimensional gel electrophoresis or they have an interesting pattern of expression along several samples in a trancriptomic analysis. From this list of proteins/​genes you want to find out whether they have something in common in terms of functionality. The lits have been selected under some particular reason that a priori may suggest that they migth be functionaly related. There are several programs/​tools that try to extract those functionalities that are behind the set of genes/​proteins,​ FatiGO or Marmite are two examples (find them within Babelomics. SNOW is another program with this aim, its particularity is that it uses protein-protein interaction data and evaluates protein/​gene modules with a structural component.
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   - Press submit and wait until the results is finished. A normal job may last aproximately less than a minute but the time may vary depending on the size of the list.    - Press submit and wait until the results is finished. A normal job may last aproximately less than a minute but the time may vary depending on the size of the list. 
  
-**1.4. Some constraints:​** ​If By now SNOW accepts lists in the range of 3 to 500 proteins/​genes mapped into the interactome of reference. +**1.4. Some constraints:​** ​Currently ​SNOW accepts lists in the range of 3 to 500 proteins/​genes ​that can be mapped into the reference ​interactome. 
-**1.5. Proteins?GEnes ids supported:​**+ 
 +**1.5. Proteins/Gene IDs supported:​**
     * affy_focus     * affy_focus
     * affy_hcg110     * affy_hcg110
snow.txt · Last modified: 2010/05/31 13:00 by jsantoyo
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