Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

BMC Bioinformatics

Table 1 Yeast protein-domain annotation data from six publicly available annotation databases

Database	N _P		N _S		N _O	N _U	A _D
Database	n	%	n	%	N _O	N _U	A _D
PFAM-A	4,709	80.0	1,174,333	40.2	2,595	2,553	1.05
SF	3,651	62.1	962,602	33.0	1,355	1,307	0.79
SMART	3,023	51.4	455,523	15.6	392	379	0.66
PRODOM	146	2.5	19,760	0.7	111	111	0.02
TIGRFAM	3,019	51.3	546,226	18.7	2,544	1,944	1.25
CDD	2,210	37.6	560,299	19.2	3,300	731	0.58

A total of 5,884 proteins containing a total of 2,921,809 amino acids were downloaded from the Saccharomyces Genome Database[31]. N_P, proteins with at least one domain annotation. N_S, protein-domain amino acid sequence coverage. N_O, number of unique domains in the original database. N_U, number of unique domains in the unified database. A_D, average number of domains per protein in the unified database.

ISSN: 1471-2105