Table 1

The enrichment of molecular functions in the urancestral FSF sets

Urancestor

Functional sub-categories (categories)

Urancestral FSFs (sample)

Extant FSFs (bkgd)

Rate for sample

Rate for bkgd

Ratio

P value


min_set

Transferases (Metabolism)

6

29

0.066

0.020

4.19

0.0021

Small molecule binding (General)

4

22

0.057

0.016

3.68

0.021

Nucleotide m/tr (Metabolism)

7

29

0.100

0.020

4.88

0.00037

max_set

Translation (Information)

34

89

0.224

0.063

3.56

E-12

Nucleotide m/tr (Metabolism)

8

29

0.053

0.020

2.57

0.0083


We evaluated which of 49 sub-categories are enriched by the min_set or the max_set. In the table, sample means the min_set (70 FSFs) or max_set (152 FSFs). The 1,416 FSFs represent the background (bkgd). For convenience, let us assume that M and k represent the number of FSFs that are assigned to a particular sub-category in the background (extant FSFs) and sample (urncestral FSFs) and N and n are the total numbers of FSFs in the background and sample without functional categorizations. The rates for the sample and the background are notated by k/n and M/N, respectively. The ratio was determined by dividing the sample rate by the background rate. The P values were calculated using the hypergeometric distribution. The enrichment of the sub-categories that are listed was supported at the 95% confidence level.

Kim and Caetano-Anoll├ęs BMC Evolutionary Biology 2011 11:140   doi:10.1186/1471-2148-11-140

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