Table 2

Average Number of YPD and GO Annotation Terms in Complex Sets.

Data Set

YPD Functions

YPD Roles

GO Components

GO Processes


MCODE on All Yeast Interactions

0.58

0.89

0.39

0.59

MIPS Complex Database

0.50

0.75

0.39

0.48

MCODE Random Model (100 AllYeast network permutations)

0.72

1.24

0.52

0.85


The average number of YPD and GO functional annotation terms per protein in an MCODE predicted complex is shown for MCODE predicted complexes on the AllYeast set, the MIPS complex database and the MCODE random model. A lower number indicates that the complexes from a set contain more functionally related proteins (or unannotated proteins). In the cases of multiple annotation, all terms are taken into account. Even though there are multiple annotation terms per protein and a variable amount of unannotated proteins per complex, these numbers should perform well in relative comparisons based on the assumption that the distribution of the latter two factors is similar in each data set.

Bader and Hogue BMC Bioinformatics 2003 4:2   doi:10.1186/1471-2105-4-2

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