Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP

Table 6 Summary of increase in annotation in genomic windows.

Organism	Total # of windows ^a)	Prior un-annotated windows ^b)	Prior un-annotated windows which are annotated by PFP	Total # of GO terms added by PFP to prior un-annotated windows ^c)	# of prior annotated windows ^d)	# of prior annotated windows to which more GO terms are predicted by PFP	# of GO terms added to the prior annotated windows
E. coli	27,840	4,436	38	142	23,404	917	1750
S. cerevisiae	48,260	4,807	29	111	43,453	670	925
P. falciparum	45,036	6,539	2418	17435	38,497	2735	17286

a) These numbers include windows with genes on the plus strand, those with genes on the minus strand, and those with genes from the both strands.
b) The number of windows which include only unannotated genes in the GOA database.
c) Only overrepresented GO terms are considered.
d) The number of windows which all the included genes are unannotated in the GOA database.

ISSN: 1471-2105