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Fisher's Exact Test

Estimate probability of the motif and keyword association

After entering the numerical values into the 2x2 contingency table click on "Calculate Fisher's Exact Test" button

          

Contingency table
                              X1 Keyword                     X2 No Keyword          
 
Y1 Motif
Y2 No Motif
  Two sided test

          

Example: Calculating keyword, motif association


Using keyword association to provide surrogate significance. 
The EH1 motif is found in some transcription factors where it provides a 
repressive function by binding to the Groucho/TLE1 repressor. Copley reported 
new EH1 motifs which he justified on the grounds that they were enriched in 
certain transcriptional keywords (PMID:16309560). 

Using our SIRW server with the Lig_EH1 regular expression from ELM, we can attempt to repeat 
his findings. SIRW allows combined  keyword + RegExp searches. The probability 
of an association can be estimated by the Fisher Exact Test or the related Hypergeometric 
Distribution. Both should be in any statistical package (such as R, Mathematica). 
See the Wikipedia entries for more info on these tests.

Open SIRW, select Uniprot_human and then pagequery. 
Type "human" in the Species field and then cut and paste the EH1 motif into the 
Pattern field. Click Do Query, then be patient while the result loads. This search 
gives you two numbers: The total sequences and the subset matching the motif. Now type 
in "HOX" in the Link field and repeat the search. This gives you two more numbers: 
The number of sequences known to have a HOX domain and the subset that match the motif.

Question:
        *   Is EH1 more or less frequent in HOX proteins? 

Repeat with different domain class keywords BZIP, TBOX, ZnF_C2H2, PAS.

Questions:

        *   Is EH1 found more, less or at the expected frequency in these transcription 
            factor classes? 
        *   How would you explain it, if any classes disfavour EH1?  
        *   Do you think keyword associations can indicate that (most) of these motifs 
            are functional?
Now Calculate the probability 
You must first use the SIRW numbers to calculate the 4 exclusive pots for the 2X2 
contingency matrix (the four permutations with/without keyword and with/without motif).

Enter the numbers and press the calculate_Fishers_Exact_Test button.
How significant are the enrichments and reductions?
Suggestion, feedback ? Contact: Chenna Ramu