ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes

Table 7 Estimation of the subcellular proteomes of eight eukaryotic organisms

	Yeast (S. cerevisiae)	Worm (C. elegans)	Fruitfly (D. melano)	Mosquito (A. gambiae)	Zebrafish (D. rerio)	Chicken (G. gallus)	Mouse (M. musculus)	Human (H. sapiens)	Range
Proteome	5,799	22,400	13,649	15,145	13,803	5,394	33,043	38,149
GO annotated	5,486	12,357	9,997	8,847	10,106	4,363	23,744	24,638
% ngLOC coverage	97.48	94.92	96.73	97.94	98.64	9,9.82	94.79	94.52	94.79-99.82
Proteome estimated	5,653	21,262	13,203	14,833	13,616	5,384	31,320	36,059
% CYT	15.22	14.80	12.74	14.43	15.01	13.66	13.44	14.14	12.74-15.22
% CSK	1.07	1.19	1.05	1.11	1.31	1.24	1.50	1.48	1.05-1.50
% END	2.71	3.47	2.85	3.25	3.34	2.53	2.99	3.04	2.53-3.47
% EXC	8.88	12.60	12.26	14.28	9.91	12.65	11.52	11.71	8.88-14.28
% GOL	1.48	1.31	1.40	1.07	1.68	1.47	1.52	1.56	1.07-1.68
% LYS	0.11	0.58	0.55	0.53	0.65	0.44	0.59	0.67	0.11-0.67
% MIT	9.55	5.84	4.86	5.52	4.72	4.16	4.24	4.80	4.16-9.55
% NUC	33.53	29.75	37.38	29.50	30.31	28.24	27.35	28.38	27.35-37.38
% PLA	16.19	24.41	20.06	21.36	21.66	22.78	27.18	24.08	16.19-27.18
% POX	0.54	0.66	0.42	0.48	0.51	0.25	0.44	0.46	0.25-0.66
% Single-localized	89.29	94.60	93.59	91.53	89.11	87.42	90.77	90.32
% Multi-localized	10.71	5.40	6.41	8.47	10.89	12.58	9.23	9.68
% CYT-NUC	6.49	2.36	2.76	3.44	5.40	6.27	4.51	4.74

This chart presents the location-wise percentages of the proteome predicted to localize into one organelle. (For example, 9.55% of the yeast proteome is localized to the mitochrondria only.) These percentages sum to the total size of the proteome estimated to be single-localized. We also present the estimated percentage of the proteome that is localized to multiple organelles. The percentage of the proteome estimated to localize to both the cytoplasm and nucleus is also displayed. The coverage is determined with a confidence score (CS) threshold of 15. Multi-localized sequences are determined with a multi-localized confidence score (MLCS) threshold of 60. CSK, cytoskeleton; CYT, cytoplasm; END, endoplasmic reticulum; EXC, extracellular; GO, Gene Ontology; GOL, golgi; LYS, lysosome; MIT, mitochondria; NUC, nucleus; PLA, plasma membrane; POX, perixosome.

ISSN: 1474-760X