Table II. Summary of correctable annotations.
Only those markers that are unequivocally annotated as located in alternative organelles are listed. Nuc, nucleus; PM, plasma membrane; Mito, mitochondrion; Cyto, cytoplasm.
| Marker |
Observed location |
Annotated locations |
|||||
|---|---|---|---|---|---|---|---|
| Gene symbol | Accession no. | Protein | Fraction | Relative abundancea | Organelle | Relative abundanceb |
|
| Control | Kdo | ||||||
| Hist1h1e | IPI00223714 | Histone H1.4 | ER | 1 | Nuc | 0.29 ± 0.07, n = 2 | 0.22 ± 0.01, n = 2 |
| Tmem48 | IPI00165794 | Nucleoporin NDC1 | ER | 1 | Nuc | 0.26, n = 1 | 0.18, n = 1 |
| Krt1 | IPI00625729 | Keratin, type II cytoskeletal 1 | ER | 1 | PM | 0.55, n = 1 | 0.22, n = 1 |
| Clptm1 | IPI00121627 | Cleft lip and palate transmembrane protein 1 homolog | ER | 1 | PM | 0.63 ± 0.19, n = 3 | 0.48 ± 0.05, n = 3 |
| Ubxd8 | IPI00265386 | Isoform 1 of Ubiquitin regulatory X (UBX) domain-containing protein 8 | ER | 1 | Cyto | 0.01, n = 1 | 0.03, n = 1 |
| Srgap2 | IPI00652316 | Slit/Robo Rho GTPase-activating protein 2 isoform 10 | PM | 1 | Mito | 0.06, n = 1 | 0.05, n = 1 |
| Preb | IPI00124980 | Prolactin regulatory element-binding protein | PM | 1 | ER | 0.48 ± 0.15, n = 3 | 0.60 ± 0.21, n = 3 |
| Nuc | 0.17, n = 1 | 0.23, n = 1 | |||||
| Coro1b | IPI00124819 | Coronin-1B | PM | 1 | Cyto | 0.15, n = 1 | 0.04, n = 1 |
| Lgals9 | IPI00114396 | Isoform long of Galectin-9 | PM | 1 | Cyto | 0.19 ± 0.05, n = 3 | 0.08 ± 0.05, n = 3 |
| Pcna | IPI00113870 | Proliferating cell nuclear antigen | Cyto | 1 | Nuc | 0.30 ± 0.04, n = 3 | 0.16 ± 0.03, n = 3 |
a Relative abundances reflect normalized marker distributions between locations. Relative abundance in main organelle is 1 by definition (see text for detail).
b Relative abundances observed in locations listed in the databases (annotated locations). Note the relatively low levels of the markers in these locations with the exception of ER proteins in plasma membrane fraction and vice versa. The latter is consistent with the distribution of the ER and plasma membrane marker ensembles as whole (Fig. 5C), resulting from cross-contamination of these two fractions (Fig. 6).