. Author manuscript; available in PMC: 2009 Nov 5.

Published in final edited form as: Proteomics Clin Appl. 2009 Jan 1;3(1):116–134. doi: 10.1002/prca.200800140

Table 2.

Sequence features of saliva and plasma proteomes and overlapping proteins between saliva and plasma

Source	Swiss_Prot_Annotation^a) (saliva: 1436; plasma: 1966; overlapped: 395)				Sequence feature predication^b) (saliva: 1939; plasma: 2720; overlapped: 597)

	Signal	Target	GlycSite	Transmem	Signalp		Targetp RC ≤2	TMHMM

					p ≥0.99	p ≥0.75
Saliva	380 (27%)	47 (3.3%)	348 (24%)	153 (10.7%)	553 (29%)	667 (34%)	211 (11%)	260 (13%)
Plasma	457 (23%)	25 (1.3%)	513 (26%)	350 (18%)	530 (20%)	702 (26%)	291 (115%)	457 (17%)
Overlap	135 (34%)	4 (1.0%)	129 (33%)	38 (9.6%)	233 (39%)	259 (43%)	73 (12%)	58 (9.7%)

^a)

Sequence feature information extracted from the UniProt knowledgebase. The number represents the proteins with the entry in the UniProt. Signal: protein with a signal sequence (prepeptide); Target: protein with a transit peptide (mitochondrion, chloroplast, thylakoid,cyanelle, or microbody); Transmem: protein with transmembrane domain; GlycSite: protein with glycosylation site.

^b)

Sequence feature information obtained from signalp, targetp, and TMHMM sequence feature prediction programs. The number represents the total proteins used for the predictions. p: HMM signal peptide probability; RC: reliability classes.