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simple_enrichment_analysis [2012/04/20 18:41]
mbleda
simple_enrichment_analysis [2012/04/20 18:50] (current)
mbleda [Simple enrichment analysis]
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 For every gene in the input list REANTO extract its annotated regulators in the selected database. Then a **[[wp>​Fisher'​s exact test]]** using a 2×2 contingency tables is used to check for significant over-representation of each regulatory element in the gene list with respect to the regulation in the genome. In the following figure we try to summarize this process. Our gene list contains targets for GATA1 (orange balls) and SP1 (blue balls) transcription factors (TFs). For each TF, we extract the proportion of targets in the gene list and in the genome to construct the contingency table. Fisher'​s exact test is used to determine if there is a nonrandom association between the gene list and the specific regulation of a TF. For every gene in the input list REANTO extract its annotated regulators in the selected database. Then a **[[wp>​Fisher'​s exact test]]** using a 2×2 contingency tables is used to check for significant over-representation of each regulatory element in the gene list with respect to the regulation in the genome. In the following figure we try to summarize this process. Our gene list contains targets for GATA1 (orange balls) and SP1 (blue balls) transcription factors (TFs). For each TF, we extract the proportion of targets in the gene list and in the genome to construct the contingency table. Fisher'​s exact test is used to determine if there is a nonrandom association between the gene list and the specific regulation of a TF.
  
 +The process is analog for miRNAs.
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 {{ :​images:​methods:​fatigo.png?​600 |FatiGO}} {{ :​images:​methods:​fatigo.png?​600 |FatiGO}}
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-The process is analog for miRNAs. 
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 ====== Multiple testing correction ====== ====== Multiple testing correction ======
simple_enrichment_analysis.txt · Last modified: 2012/04/20 18:50 by mbleda
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