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

Hawkins, Troy; Chitale, Meghana; Kihara, Daisuke

doi:10.1186/1471-2105-11-265

Table 7 Examples of windows with newly annotated highly similar genes.

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

Organism	Position	Direction ^a)	# of Proteins (Average *FunSim*)	New annotations (GO)	P-value ^b)
E. coli	1212000 (bp)	Both	11 (0.792)	Regulation of biological process (0050789)	0.00006
				Intracellular membrane-bound organelle (0043231)	0.0000005
				Membrane-bound organelle (0043227)	0.0000005
				Intracellular organelle (0043229)	0.000004
	3016000	both	7 (0.711)	Transport (0006810)	0.002
				Establishment of localization (0051234)	0.002
yeast	chr07 798000 (bp)	minus	2 (0.793)	rRNA processing (0006364)	0.001
	chr02 165000	both	7 (0.704)	Organelle lumen (0043233)	0.001
				Membrane-enclosed lumen (0031974)	0.001
	chr14 141000	Plus	3 (0.749)	Chromatin silencing at telomere (0006348)	0.0004
				Telomeric heterochromatin formation (0031509)	0.0004
	chr15 342000	both	6 (0.760)	Signal transducer activity (0004871)	0.001
				Transmembrane receptor activity (0004888)	0.00007
				Receptor activity (0004872)	0.0002
malaria	chr03 906000	both	6 (0.722)	Phosphotransferase activity, alcohol group as acceptor (0016773)	0.001
				Transferase activity, transferring phosphorus-containing groups (0016772)	0.002
	chr06 6000	both	5 (0.891)	NADPH regeneration (0006740)	0.0001
				NADPH metabolism (0006739)	0.0001
				Nicotinamide metabolism (0006769)	0.0001
				Pyridine nucleotide metabolism (0019362)	0.0002
				Oxidoreduction coenzyme metabolism (0006733)	0.0004
				Water-soluble vitamin metabolism (0006767)	0.0004
	chr07 1296000	both	7 (0.866)	Dopamine receptor activity (0004952)	0.0001
				Amine receptor activity ( 0008227)	0.0001
				Neurotransmitter receptor activity (0030594)	0.0001
				Dopamine binding (0035240)	0.0001
				Rhodopsin-like receptor activity (0001584)	0.001
				Receptor activity (0004872)	0.001
				Neurotransmitter binding (0042165)	0.0001
				G-protein coupled receptor activity (0004930)	0.001
	chr09 144000	plus	3 (0.881)	RNA localization (0006403)	0.0002
	chr10 492000	minus	4 (0.860)	Mitotic cell cycle (0000278)	0.0001
				Negative regulation of transcription by carbon catabolites (0045013)	0.0004
				Regulation of transcription by carbon catabolites (0045990)	0.0004
				Response to nutrients (0007584)	0.0004
				Regulation of transcription by glucose (0046105)	0.0004
				Intracellular transport (0046907)	0.0003
				Establishment of localization in cell (0051649)	0.0003
	chr14 3174000	both	6 (0.800)	Autophagic vacuole fusion (0000046)	0.00001
				Organelle fusion (0048284)	0.00009
				Macroautophagy (0016236)	0.00002
				Autophagy (0006914)	0.00002

a) The direction of the DNA strands on which the genes are located.
b) The P-value of the overrepresentation of the GO term in the genes in the window

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Bioinformatics

Contact us