Standard name
Human Ortholog
Description Nexin-1 homolog; required for localizing membrane proteins from a prevacuolar/late endosomal compartment back to late Golgi; structural component of retromer membrane coat complex; forms a retromer subcomplex with Vps17p; required for recruiting the retromer complex to the endosome membranes; VPS5 has a paralog, YKR078W, that arose from the whole genome duplication
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Micrographs

ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 0 0 0 0.05 0.05 0.05 0.05 0 0 0.05 0 0 0 0 0 0 0 0 0 0 0 0
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.11 0 0 0 0.05 0.06 0.07 0.06 0.06 0.08 0.05 0.07 0 0 0 0.07 0 0.06 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0 0 0 0 0 0 0 0
Endosome 0.58 0.59 0.75 0.77 0.69 0.48 0.28 0.45 0.25 0.34 0.25 0.19 0.73 0.83 0.86 0.78 0.78 0.73 0.76 0.8 0.86 0.78 0.77 0.77
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0.05
Mitochondria 0.12 0.06 0.2 0.17 0.26 0.38 0.61 0.41 0.59 0.57 0.66 0.68 0 0 0 0.14 0.15 0.07 0 0 0 0 0 0
Nucleus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 0.15 0.16 0.21 0.09 0.05 0.07 0.06 0.08 0.06 0.05 0 0.06 0.15 0.12 0.21 0.2 0.3 0.26 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0.07 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0.21 0.1 0.14 0.11 0.08 0.12 0.12 0.17 0.09 0.08 0 0.06 0.27 0.28 0.28 0.34 0.29 0.26 0.05 0 0 0 0 0
Vac/Vac Membrane 0.11 0.51 0.15 0.3 0.34 0.16 0.12 0.1 0.16 0.11 0.11 0.09 0.33 0.28 0.28 0.27 0.23 0.26 0.06 0.1 0 0.07 0 0.05
ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 2 2 1 0 0 1 0 3 2 3 0 3 2 0 0 0 1 0 5 1 0 2 0 4
Bud 8 1 4 2 9 22 20 31 19 20 16 25 1 1 0 0 0 0 0 6 1 2 0 1
Bud Neck 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1
Bud Site 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
Cytoplasm 40 15 4 13 21 27 30 38 22 42 18 35 6 14 10 16 9 15 11 1 0 0 1 0
Endoplasmic Reticulum 2 1 2 1 1 5 5 4 7 6 12 12 3 1 0 11 3 8 2 0 0 5 8 4
Endosome 214 341 245 234 266 204 120 278 97 185 93 103 223 324 303 189 205 176 315 502 296 234 235 261
Golgi 5 3 2 2 0 0 0 0 0 0 1 1 1 2 1 0 1 4 11 10 6 7 15 15
Mitochondria 46 37 65 51 99 161 261 254 232 310 247 362 6 5 0 34 39 17 8 9 4 6 9 10
Nucleus 6 5 5 0 0 3 2 1 1 2 1 0 1 0 1 0 1 3 2 3 1 1 0 0
Nuclear Periphery 0 8 6 2 0 1 0 0 1 4 1 3 5 3 1 0 3 5 1 3 1 1 1 2
Nucleolus 55 92 69 27 21 30 26 51 24 29 15 33 46 47 74 48 79 62 1 4 1 1 1 1
Peroxisomes 4 1 12 13 11 14 9 44 12 10 4 9 8 13 8 3 6 4 2 3 3 1 1 3
SpindlePole 78 58 44 34 32 50 50 109 37 44 14 31 83 109 100 83 77 63 18 18 14 11 11 9
Vac/Vac Membrane 42 299 50 91 131 70 53 61 63 62 40 46 101 109 99 66 60 62 23 60 8 21 13 16
Unique Cell Count 368 581 325 305 387 425 429 623 391 546 375 529 307 391 352 242 264 240 414 632 343 301 305 340
Labelled Cell Count 502 863 509 470 591 588 576 874 517 719 464 664 486 628 597 450 484 420 414 632 343 301 305 340


Endosome

(Huh et al. Nature 2003 425:686)
Screen WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 AF100 AF140 AF180
Mean Cell GFP Intensity (1e-4) 7.8 7.8 6.4 6.5 6.0 5.6 5.0 5.4 5.1 4.9 5.0 5.1 8.2 8.0 8.5 8.8 8.9 8.9 9.1 9.2 9.2
Std Deviation (1e-4) 1.6 1.1 1.1 1.2 1.1 0.9 0.8 1.2 0.8 0.9 1.0 0.8 1.1 1.1 1.2 1.5 1.6 1.7 1.4 1.5 1.4
Intensity Change (Log2) – – – 0.03 -0.09 -0.17 -0.35 -0.22 -0.31 -0.37 -0.34 -0.31 0.37 0.33 0.42 0.47 0.48 0.48 0.52 0.54 0.53


Localization RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3
Cortical Patches 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 1.1 2.9 2.7 2.9 2.7 2.1 2.4 2.7 0 0 0 0 0 0
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 2.3 3.0 3.5 3.8 3.5 3.1 4.1 2.7 3.7 0 2.0 1.5 3.4 1.8 3.3
Endoplasmic Reticulum 0 0 0 0 0 0 0 2.4 1.8 0 0 0 3.1 0 0
Endosome 0.4 -2.0 -7.6 -12.9 -9.0 -13.5 -11.8 -13.4 -16.1 -0.8 2.5 3.5 0.8 0.6 -0.6
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria -1.1 1.8 5.3 11.2 6.4 10.6 10.6 12.2 13.7 -7.2 -8.4 -8.8 -1.8 -1.7 -4.3
Nucleus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 0 0 0 -0.2 0 0 0 0 0
Nucleolus -4.3 -6.3 -5.7 -6.2 -5.7 -6.0 -7.2 -7.0 -6.6 -2.0 -3.3 -0.1 -0.4 2.4 1.3
Peroxisomes 0.4 -0.6 -0.3 -1.3 2.1 -0.5 -1.7 -2.3 -1.8 -0.8 -0.3 -1.1 -1.8 -1.0 -1.4
SpindlePole -0.9 -2.3 -0.7 -0.8 1.6 -1.7 -2.6 -4.7 -3.8 4.2 4.7 4.7 5.9 4.7 3.8
Vacuole 4.3 5.6 0.4 -1.2 -2.5 0.3 -1.7 -1.9 -3.0 5.2 4.0 4.0 3.5 2.3 3.1

Images

Circle plot not available

Protein Concentration and Protein Localization Data

R1 R2 R3
G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase
Concentration 2.8044 3.6911 3.2409 3.1578 2.6541 3.3215 4.9833 6.6308 5.9783 5.6811 5.7497 6.0109 4.4589 5.7647 5.0977 5.1115 4.4184 5.086
Actin 0.0014 0.0001 0.0052 0.0002 0.0007 0.0001 0.0003 0.0001 0.0001 0 0 0.0021 0.0012 0 0.0006 0.0022 0 0.0002
Bud 0.0001 0.001 0.0004 0.0001 0.0001 0 0 0.0001 0 0 0 0 0.0001 0.0001 0.0002 0.0001 0 0
Bud Neck 0.0003 0.001 0.0005 0.0001 0.0006 0.0008 0.0002 0.0002 0.0002 0.0001 0.0001 0.0008 0.0015 0.0012 0.0038 0.0006 0.0011 0.0004
Bud Periphery 0.0002 0.0006 0.0004 0.0001 0.0002 0 0 0 0 0 0 0 0.0001 0.0001 0.0003 0.0001 0 0.0001
Bud Site 0.0008 0.0054 0.0014 0.0002 0.0005 0.0004 0.0003 0.0006 0.0001 0.0001 0.0001 0.0001 0.0003 0.0007 0.0019 0.0007 0.0004 0.0002
Cell Periphery 0.0001 0.0001 0.0002 0 0.0001 0.0001 0.0001 0 0 0 0.0001 0 0.0001 0.0001 0.0001 0.0001 0 0.0001
Cytoplasm 0.0029 0.017 0.0048 0.0015 0.0015 0.0022 0.0013 0.0021 0.0011 0.0013 0.0009 0.0015 0.0075 0.0036 0.0025 0.0011 0.0011 0.0016
Cytoplasmic Foci 0.1244 0.153 0.1458 0.1524 0.1355 0.1556 0.1371 0.183 0.1758 0.118 0.1064 0.1437 0.0919 0.1469 0.1178 0.0884 0.1418 0.1101
Eisosomes 0 0 0.0005 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 0 0
Endoplasmic Reticulum 0.0011 0.001 0.0013 0.0003 0.0008 0.0004 0.0005 0.0002 0.0002 0.0001 0.0004 0.0005 0.0017 0.0004 0.0004 0.0003 0.0001 0.0008
Endosome 0.6436 0.6103 0.6373 0.7223 0.5823 0.6121 0.6448 0.6042 0.6084 0.7544 0.7195 0.5768 0.7084 0.6482 0.7106 0.7994 0.762 0.6589
Golgi 0.0492 0.0364 0.0616 0.0462 0.095 0.064 0.0596 0.0809 0.0955 0.0758 0.0636 0.0861 0.041 0.0413 0.0594 0.0376 0.0495 0.0622
Lipid Particles 0.1103 0.0525 0.0638 0.018 0.0939 0.1075 0.117 0.0864 0.0755 0.018 0.0793 0.1497 0.0781 0.0764 0.0587 0.0354 0.0184 0.1053
Mitochondria 0.0099 0.001 0.0092 0.0095 0.0301 0.0014 0.0022 0.0093 0.002 0.0007 0.0005 0.0014 0.0072 0.0011 0.0031 0.0019 0.0003 0.0029
None 0.0005 0.0003 0.0034 0.0001 0.0002 0.0001 0.0001 0.0001 0.0001 0 0 0.0001 0.0046 0.0001 0.0002 0.0003 0 0.0001
Nuclear Periphery 0.0018 0.0067 0.0022 0.0003 0.0017 0.0006 0.004 0.0001 0.0002 0.0001 0.0004 0.0033 0.0026 0.0006 0.0015 0.0003 0.0001 0.003
Nucleolus 0.0004 0.0018 0.0009 0.0001 0.0007 0.0019 0.0004 0.0007 0.0001 0.0002 0.0001 0.0003 0.0019 0.0031 0.0007 0.0004 0.0014 0.0009
Nucleus 0.0003 0.002 0.0015 0.0001 0.0006 0.0004 0.0001 0.0001 0.0001 0.0001 0.0001 0.0002 0.0037 0.0005 0.0023 0.0001 0.0001 0.0012
Peroxisomes 0.0294 0.0138 0.0233 0.0085 0.0257 0.0167 0.0152 0.0213 0.023 0.0067 0.0053 0.0164 0.0095 0.0091 0.01 0.0091 0.0089 0.0103
Punctate Nuclear 0.0019 0.0012 0.0017 0.0002 0.0013 0.0049 0.0025 0.0005 0.0014 0.0001 0.0002 0.0008 0.0025 0.003 0.001 0.0006 0.0008 0.0012
Vacuole 0.0164 0.0832 0.0285 0.0337 0.0205 0.0251 0.0104 0.0068 0.0126 0.0209 0.0191 0.0115 0.0284 0.0538 0.0196 0.0165 0.0104 0.0312
Vacuole Periphery 0.0048 0.0114 0.0062 0.0062 0.0081 0.0059 0.0038 0.0031 0.0036 0.0032 0.0039 0.0046 0.0076 0.0097 0.0052 0.0049 0.0034 0.0092

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 21.2193 14.5914 22.7376 20.8478 15.8722 26.1016 19.6711 21.9065 23.3898 20.2773
Translational Efficiency 1.4998 2.1066 1.2879 1.7507 1.8614 1.3743 1.5142 1.6945 1.569 1.4398

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Nexin-1 homolog; required for localizing membrane proteins from a prevacuolar/late endosomal compartment back to late Golgi; structural component of retromer membrane coat complex; forms a retromer subcomplex with Vps17p; required for recruiting the retromer complex to the endosome membranes; VPS5 has a paralog, YKR078W, that arose from the whole genome duplication
Localization
Cell Percentages endosome (44%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Vps5

Vps5


Nearest neighbours ( genes)

correlation threshold

0.6

1.0

0.80


Biological Process (Gene Ontology)
Molecular Function (Gene Ontology)
Cellular Component (Gene Ontology)

Endocytosis
Temp Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Vph1-GFP)
37℃
RT
Cell Cycle Omics

CYCLoPs (Vps5-GFP)
Gene / Allele Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Sac6-tdTomato)
Gene Images
Gene Images
Images are not yet available
Images are not yet available