Characterization of the predicted surfaceome.
(A–C) Comparison of 2,886 surfaceome proteins in red, with 2,216 nonsurfaceome membrane proteins in blue.
(A) Distributions of sequence features in noncytoplasmic domains of surfaceome (upper graphs) and nonsurfaceome membrane (lower graphs)
proteins, calculated as frequency per 100 amino acids.
A, Left shows the distribution of numbers of N-glycosylation sequence motifs (N-X-S/T) per 100 amino acids.
Proteins with more than five motifs were excluded from this graph.
A, Center shows the distribution of numbers of C-glycosylation sites per 100 amino acids predicted by using GlycoMine.
Proteins with more than four predicted sites were excluded.
A, Right shows the distribution of numbers of cysteine residues per 100 amino acids.
Proteins with >10 cysteines were excluded.
(B) Distribution of the number of ɑ-helical TM domains per protein.
The pie chart shows the proportion of GPCRs within the set of surface proteins with seven TM domains (red bar).
(C) Distribution of the length of ɑ-helical TM domains.
(D) Classification of surface and nonsurface proteins into functional classes. *P < 10−2.
Functional classes are numbered as follows: 1, GPCRs; 2, receptor-type tyrosine kinases; 3, receptors of the Ig superfamily;
4, scavenger receptors; 5, other receptors; 6, channels; 7, solute carrier superfamily; 8, active transporters;
9, auxiliary transport proteins; 10, other transporters; 11, oxidoreductases; 12, transferases; 13, hydrolases;
14, lyases; 15, isomerases; 16, ligases; 17, structure/adhesion proteins; 18, ligand proteins; and 19, proteins of unknown function.
(E) Overlap of proteins of the human surfaceome annotated in UniProt, predicted by YLoc (13), predicted by da Cunha et al. (17), and predicted by SURFY.
(F) Protter image of human MEGF9. N-X-S/T motifs are marked in light blue, with the corresponding asparagine (N) in dark blue.
CSC identified peptides are marked in purple.
(G) Half-life distributions of surfaceome proteins, transcription factors (TF), and all quantified proteins from Beck et al. (65). Misc., miscellaneous.