Standard name
Human Ortholog
Description Endosomal Rab family GTPase; required for endocytic transport and sorting of vacuolar hydrolases; required for endosomal localization of the CORVET complex; required with YPT52 for MVB biogenesis and sorting; involved in autophagy and ionic stress tolerance; geranylgeranylation required for membrane association; protein abundance increases in response to DNA replication stress; mammalian Rab5 homolog; VPS21 has a paralog, YPT53, 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
Bud 0 0 0 0 0 0 0 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
Bud Site 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 – 0 0.05 0.05 0 – 0 – – – 0 0 0 0 0 0
Cytoplasm 0.99 1.0 0.98 0.97 0.97 0.94 0.86 0.87 – 0.88 0.79 0.87 0.95 – 1.0 – – – 0.98 0.99 0.96 0.95 0.86 0.87
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Endosome 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Mitochondria 0 0 0 0 0 0 0 0 – 0 0.13 0.12 0.05 – 0 – – – 0 0 0 0 0 0
Nucleus 0 0 0 0 0 0 0 0 – 0 0 0 0.05 – 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
Nucleolus 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Vac/Vac Membrane 0 0 0 0 0 0 0.09 0 – 0.08 0.05 0 0 – 0 – – – 0 0 0 0 0 0
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 1 1 0 5 – 4 0 0 0 – 0 – – – 0 0 0 0 0 0
Bud 0 0 0 0 0 1 0 2 – 0 0 1 0 – 0 – – – 0 0 1 0 1 0
Bud Neck 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 – – – – – – – – –
Cell Periphery 1 0 1 1 0 7 5 5 – 2 6 6 0 – 0 – – – 0 0 0 0 0 0
Cytoplasm 135 196 130 131 118 149 138 167 – 96 101 105 19 – 44 – – – 131 193 130 26 48 68
Endoplasmic Reticulum 0 1 0 1 1 4 6 8 – 1 4 0 0 – 0 – – – 0 0 0 0 0 0
Endosome 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Mitochondria 0 0 1 1 1 1 4 4 – 2 17 14 1 – 0 – – – 0 0 0 0 0 0
Nucleus 1 0 1 2 1 2 0 6 – 1 1 3 1 – 0 – – – 0 1 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 0 0 – 0 1 0 0 – 0 – – – 0 0 0 0 0 0
Nucleolus 0 0 0 0 0 0 0 0 – 0 1 0 0 – 0 – – – 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 1 0
SpindlePole 0 0 0 0 0 0 0 0 – 0 0 0 0 – 0 – – – 0 0 0 0 0 0
Vac/Vac Membrane 0 0 0 1 1 1 15 8 – 9 6 5 0 – 0 – – – 0 0 1 0 0 3
Unique Cell Count 136 196 132 135 122 159 160 193 109 128 121 20 44 135 196 135 28 56 78
Labelled Cell Count 137 197 133 137 123 166 168 205 115 137 134 21 44 135 196 135 28 56 78


Cytoplasm, Nucleus

(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) 26.1 27.8 17.8 17.3 18.1 18.0 18.6 18.3 – 16.0 17.9 17.1 18.6 – 24.7 – – – – 25.0 26.0
Std Deviation (1e-4) 3.7 3.6 3.5 4.5 4.5 4.8 4.5 5.5 – 4.7 5.5 4.6 3.8 – 4.3 – – – – 4.9 9.8
Intensity Change (Log2) – – – -0.04 0.02 0.02 0.06 0.04 – -0.15 0.0 -0.06 0.06 – 0.47 – – – – 0.49 0.54


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 – – –
Bud 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Bud Neck 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Bud Site 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Cell Periphery 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Cytoplasm -0.8 -0.9 -2.0 -3.8 -3.8 – -3.3 -5.0 -3.6 -1.0 – 0.8 – – –
Endoplasmic Reticulum 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Endosome 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Golgi 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Mitochondria 0 0 0 0 0 – 0 4.0 3.6 0 – 0 – – –
Nucleus 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Nuclear Periphery 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Nucleolus 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Peroxisomes 0 0 0 0 0 – 0 0 0 0 – 0 – – –
SpindlePole 0 0 0 0 0 – 0 0 0 0 – 0 – – –
Vacuole 0 0 0 3.6 0 – 0 0 0 0 – 0 – – –

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 17.1591 21.2319 18.5264 17.0159 16.8619 19.0361 15.4217 20.695 20.9229 19.8221 18.856 19.0809 18.3737 21.6714 20.108 19.8948 19.449 20.2961
Actin 0.0096 0.0002 0.0031 0.0027 0.0042 0.0007 0.008 0.0002 0.0038 0.0002 0.0034 0.0024 0.0185 0.0003 0.0017 0.0005 0.0122 0.0068
Bud 0.0003 0.0001 0.0005 0.0005 0.0002 0.0002 0.0015 0 0.0006 0.0001 0.0015 0.0003 0.0006 0.0001 0.0001 0.0001 0.0001 0.0007
Bud Neck 0.0004 0.0001 0.0004 0.0007 0.0005 0.001 0.0011 0.0001 0.0004 0.0009 0.0006 0.0008 0.0009 0.0002 0.0002 0.0003 0.0004 0.0009
Bud Periphery 0.0002 0 0.0008 0.0011 0.0002 0.0001 0.0019 0 0.0004 0 0.0005 0.0004 0.0004 0 0.0001 0 0.0001 0.0005
Bud Site 0.0007 0.0001 0.0015 0.0031 0.0004 0.0001 0.0021 0 0.0106 0 0.0003 0.0001 0.0008 0.0001 0.0004 0 0.0003 0.0003
Cell Periphery 0.0001 0 0.0002 0.0006 0.0001 0 0.0008 0 0 0 0 0.0001 0.0001 0 0 0 0.0001 0.0001
Cytoplasm 0.8419 0.9854 0.9455 0.8514 0.8888 0.9239 0.7877 0.9844 0.9574 0.9865 0.9671 0.9428 0.8788 0.9862 0.9519 0.9308 0.9352 0.9223
Cytoplasmic Foci 0.0257 0.0005 0.005 0.0069 0.0136 0.005 0.0159 0.0005 0.0092 0.0009 0.0022 0.0016 0.012 0.0006 0.0069 0.0012 0.0048 0.0024
Eisosomes 0.0001 0 0.0002 0.0002 0 0 0 0 0 0 0 0 0.0002 0 0 0 0.0004 0
Endoplasmic Reticulum 0.014 0.0005 0.002 0.002 0.0082 0.0032 0.0274 0.0003 0.0007 0.0006 0.0013 0.0024 0.0042 0.0004 0.0008 0.0005 0.0026 0.0019
Endosome 0.021 0.0002 0.0037 0.025 0.0154 0.0038 0.0283 0.0001 0.0014 0.0002 0.0018 0.008 0.0128 0.0002 0.0059 0.0021 0.0072 0.0086
Golgi 0.0042 0 0.0011 0.0044 0.0054 0.0004 0.0041 0 0.0008 0 0.0003 0.0041 0.0038 0 0.001 0.0021 0.0042 0.0027
Lipid Particles 0.0145 0 0.0053 0.0206 0.0129 0.002 0.0016 0 0.0008 0 0 0.0018 0.0131 0 0.0046 0.0435 0.0047 0.001
Mitochondria 0.0027 0.0001 0.0115 0.0373 0.0035 0.0012 0.0029 0 0.0002 0.0001 0.0023 0.0035 0.0045 0.0001 0.0024 0.0015 0.0058 0.0031
None 0.006 0.0003 0.0008 0.0022 0.0056 0.0008 0.0065 0.0003 0.0009 0.0005 0.0012 0.001 0.0018 0.0005 0.0021 0.0002 0.0019 0.001
Nuclear Periphery 0.0104 0.0014 0.0022 0.0038 0.0082 0.0132 0.0286 0.0009 0.0012 0.0013 0.0017 0.0084 0.0078 0.0014 0.0017 0.0017 0.0025 0.0088
Nucleolus 0.0002 0 0.0004 0.0009 0.0003 0.0002 0.0006 0 0.0001 0 0 0.0001 0.0005 0 0.0001 0.0001 0 0.0002
Nucleus 0.0311 0.0107 0.0124 0.0135 0.0248 0.0372 0.0493 0.0129 0.0081 0.0083 0.0145 0.0194 0.0231 0.0093 0.0125 0.009 0.015 0.0322
Peroxisomes 0.0072 0 0.0016 0.004 0.0012 0.0008 0.0006 0 0.0009 0 0.0002 0.0003 0.0089 0 0.0038 0.0042 0.001 0.0008
Punctate Nuclear 0.0031 0.0001 0.0005 0.0015 0.0016 0.0042 0.0107 0.0002 0.0024 0.0002 0.0004 0.0011 0.0015 0.0002 0.0028 0.0005 0.0003 0.0042
Vacuole 0.0048 0.0003 0.001 0.0135 0.0036 0.0012 0.0164 0 0.0002 0.0002 0.0004 0.0008 0.0044 0.0001 0.0008 0.0011 0.0009 0.0008
Vacuole Periphery 0.0017 0.0001 0.0005 0.004 0.0014 0.0006 0.0039 0 0.0001 0 0.0002 0.0006 0.0012 0 0.0001 0.0004 0.0004 0.0005

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 20.0461 35.8399 26.5947 38.2117 30.5107 15.6795 29.5416 37.2187 43.8514 35.3087
Translational Efficiency 4.3774 2.4273 2.8332 2.3644 2.5461 4.9739 2.8008 1.907 1.8702 2.3723

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✔
Translational Efficiency ✘

Micrographs

Cell Count

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
164 1099 2785 1127 1341 71 2325 61 1505 1170 5110 1188

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 1419.86 1719.24 2280.58 2789.92 1528.29 1778.88 2610.01 2922.00 1516.47 1722.86 2430.47 2796.70
Standard Deviation 309.37 323.51 489.84 564.35 325.18 282.58 463.83 467.53 325.26 321.49 505.54 560.54
Intensity Change Log 2 — 0.276022 0.683652 0.974475 — 0.219051 0.772137 0.935038 — 0.246770 0.730199 0.954166

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000365 0.000208 0.000031 0.015224 0.000212 0.000329 0.000051 0.002091 0.000229 0.000216 0.000040 0.014549
Bud Neck 0.001424 0.000424 0.000284 0.001875 0.000328 0.001169 0.000867 0.027638 0.000447 0.000469 0.000550 0.003198
Bud Site 0.012064 0.001694 0.000318 0.007828 0.002581 0.004888 0.002339 0.005698 0.003615 0.001888 0.001237 0.007719
Cell Periphery 0.000220 0.000083 0.000045 0.000320 0.000196 0.000137 0.000058 0.000447 0.000199 0.000087 0.000051 0.000327
Cytoplasm 0.845849* 0.794023* 0.704845* 0.649375* 0.864751* 0.763433* 0.768292* 0.616325* 0.862691* 0.792167* 0.733713* 0.647678*
Cytoplasmic Foci 0.028591 0.005658 0.001322 0.009410 0.005689 0.028338 0.002029 0.026626 0.008184 0.007034 0.001644 0.010294
Eisosomes 0.000004 0.000001 0.000000 0.000005 0.000002 0.000005 0.000001 0.000052 0.000002 0.000002 0.000000 0.000008
Endoplasmic Reticulum 0.000896 0.000306 0.000018 0.000105 0.000389 0.000343 0.000020 0.001599 0.000444 0.000309 0.000019 0.000181
Endosome 0.000987 0.000220 0.000018 0.001884 0.000258 0.004801 0.000069 0.029069 0.000338 0.000498 0.000042 0.003280
Golgi 0.001123 0.000282 0.000067 0.002803 0.000853 0.005288 0.000084 0.001193 0.000883 0.000585 0.000075 0.002720
Lipid Particles 0.000442 0.000207 0.000068 0.000760 0.000226 0.000508 0.000187 0.038620 0.000249 0.000225 0.000122 0.002704
Mitochondria 0.000356 0.000073 0.000119 0.000223 0.000178 0.008496 0.000135 0.005461 0.000197 0.000584 0.000126 0.000492
Mitotic Spindle 0.004492 0.003595 0.000748 0.013024 0.000961 0.037026 0.007977 0.014033 0.001346 0.005623 0.004037 0.013076
None 0.004852 0.014342 0.013399 0.023093 0.007244 0.007476 0.013442 0.005216 0.006983 0.013925 0.013418 0.022175
Nuclear Periphery 0.000087 0.000067 0.000083 0.000162 0.000048 0.000244 0.000129 0.002818 0.000052 0.000078 0.000104 0.000298
Nuclear Periphery Foci 0.003028 0.002676 0.000198 0.001395 0.002390 0.002949 0.000349 0.014140 0.002459 0.002692 0.000267 0.002050
Nucleolus 0.000127 0.000219 0.000062 0.000140 0.000176 0.000177 0.000187 0.002724 0.000171 0.000216 0.000119 0.000273
Nucleus 0.074024 0.168728* 0.275952* 0.262283* 0.107015 0.101592 0.198461* 0.172739* 0.103420 0.164654* 0.240694* 0.257685*
Peroxisomes 0.000136 0.000033 0.000004 0.000439 0.000040 0.000401 0.000033 0.008663 0.000050 0.000055 0.000017 0.000861
Vacuole 0.018939 0.006946 0.002398 0.009370 0.005957 0.021220 0.005238 0.022638 0.007372 0.007813 0.003690 0.010052
Vacuole Periphery 0.001996 0.000214 0.000023 0.000283 0.000507 0.011180 0.000051 0.002210 0.000669 0.000880 0.000036 0.000382

Localization Changes (T-score)

R1 R2 R1 & R2
UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14
Actin 1.12 4.04 -2.22 -2.26 -2.38 -1.22 3.63 -1.04 -0.45 -1.71 -0.70 5.14 -2.28 -2.27 -2.38
Bud Neck 3.64 3.57 -2.45 -7.57 -7.52 -3.50 -6.79 -1.81 -1.45 -1.39 -1.58 -5.44 -7.77 -7.33 -5.96
Bud Site 4.45 5.21 2.86 -4.31 -7.11 -1.60 0.72 -3.27 -0.94 -4.00 2.21 3.91 -1.90 -4.35 -6.10
Cell Periphery 2.60 3.39 -5.27 -10.36 -11.29 0.42 0.72 -3.32 -4.10 -4.41 1.30 1.36 -3.96 -10.89 -11.12
Cytoplasm 2.33 9.78 14.07 23.20 10.31 3.38 28.78 8.85 3.98 3.13 12.08 36.78 35.81 23.40 13.27
Cytoplasmic Foci 4.83 5.86 3.35 -5.38 -10.22 -4.01 1.56 -4.72 -0.91 -4.85 0.34 7.41 -4.88 -5.11 -10.06
Eisosomes 3.10 4.85 -1.34 -7.33 -10.47 -1.96 0.91 -1.84 -1.17 -1.96 0.22 2.40 -5.00 -6.90 -9.44
Endoplasmic Reticulum 1.66 2.69 2.53 3.10 -5.11 0.69 3.83 1.08 0.59 -1.03 1.12 4.56 3.97 3.17 -4.25
Endosome 2.96 3.83 1.34 -1.05 -1.87 -1.86 2.56 -0.96 0.12 -1.02 -0.64 4.64 -1.02 -0.70 -2.02
Golgi 2.66 3.50 0.46 -1.46 -2.08 -1.27 2.92 1.69 1.48 -2.38 1.41 3.47 0.18 -0.81 -2.05
Lipid Particles 2.35 2.78 -5.55 -7.12 -7.31 -2.92 -5.88 -1.64 -1.49 -1.51 -0.81 -3.23 -6.38 -6.26 -5.77
Mitochondria 2.39 1.55 1.45 -5.73 -0.58 -0.98 0.23 -0.83 0.89 -0.85 -0.64 0.65 -0.03 0.64 -0.97
Mitotic Spindle 0.26 2.12 -1.61 -1.71 -3.23 -1.63 -5.45 -1.69 1.46 2.19 -2.30 -4.69 -3.51 -1.03 -1.79
None -5.73 -9.08 -7.42 -0.72 -1.40 0.60 -5.85 1.64 0.36 7.57 -4.56 -8.79 -6.38 -0.75 -1.67
Nuclear Periphery 1.90 -3.28 -10.79 -16.81 -10.69 -3.06 -20.70 -2.83 -1.87 -1.77 -5.01 -23.19 -16.23 -13.89 -7.01
Nuclear Periphery Foci -0.07 2.68 1.26 3.97 -8.67 -1.68 7.95 -0.97 0.40 -2.37 -1.73 9.35 2.66 3.98 -7.74
Nucleolus -0.62 2.13 -0.84 0.45 -7.01 0.28 -0.21 -0.71 -0.84 -0.67 -0.20 0.46 0.11 0.33 -1.17
Nucleus -9.53 -23.44 -19.64 -15.38 2.21 0.63 -27.28 -3.55 -3.49 2.95 -12.12 -41.78 -27.10 -15.76 -1.19
Peroxisomes 3.75 4.91 -0.21 -2.28 -2.87 -1.57 0.89 -0.99 -0.69 -1.01 0.04 2.49 -2.14 -2.17 -2.76
Vacuole 3.04 3.62 -2.72 -13.84 -15.70 -3.36 -12.48 -5.70 -4.08 -4.83 -1.48 -3.40 -14.89 -14.26 -14.19
Vacuole Periphery 2.16 2.41 2.29 0.86 -1.65 -1.37 2.71 0.79 1.42 -1.02 0.01 3.59 3.03 1.60 -1.62
Standard name
Human Ortholog
Description Endosomal Rab family GTPase; required for endocytic transport and sorting of vacuolar hydrolases; required for endosomal localization of the CORVET complex; required with YPT52 for MVB biogenesis and sorting; involved in autophagy and ionic stress tolerance; geranylgeranylation required for membrane association; protein abundance increases in response to DNA replication stress; mammalian Rab5 homolog; VPS21 has a paralog, YPT53, that arose from the whole genome duplication
Localization
Cell Percentages cytoplasm (94%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-7

Vps21

Vps21


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 (Vps21-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