Standard name
Human Ortholog
Description Endosomal Rab family GTPase; required for vacuolar protein sorting, endocytosis and multivesicular body (MVB) biogenesis and sorting; required for localization of the CORVET complex to endosomes; involved in autophagy and ionic stress tolerance; similar to Vps21p and Ypt53p; mammalian Rab5 homolog; protein abundance increases in response to DNA replication stress
DOWNLOAD

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 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 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 0.06 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 1.0 0.99 0.96 0.99 0.97 0.97 0.87 0.86 0.81 0.78 0.8 0.83 0.99 0.99 0.99 0.94 0.99 0.9 0.96 0.98 0.94 0.93 0.92 0.94
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0.06 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 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 0 0 0 0 0
Mitochondria 0 0 0 0 0 0 0 0 0.09 0.06 0.13 0.07 0 0 0 0 0 0 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 0 0 0 0 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 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 0 0 0 0 0
Vac/Vac Membrane 0 0 0 0 0 0 0.05 0.06 0 0.09 0 0.07 0 0 0 0.06 0 0.11 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 6 0 4 2 1 0 0 0 0 1 0 0 0 0 0 0
Bud 0 0 0 0 0 0 0 3 0 0 0 4 0 0 0 0 0 0 0 0 1 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 1 7 0 2 7 5 6 13 16 11 21 7 1 1 3 7 6 2 0 0 0 0 0 0
Cytoplasm 102 262 249 194 304 299 250 470 301 202 266 299 167 251 285 240 286 172 97 255 231 115 129 180
Endoplasmic Reticulum 0 1 4 1 4 4 9 22 22 9 14 14 0 1 4 2 2 2 0 1 3 1 2 1
Endosome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 1 0 1 0
Golgi 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 0 0 0 0 1
Mitochondria 0 0 1 0 5 1 13 13 33 16 42 26 0 0 0 1 1 0 0 0 0 0 0 0
Nucleus 0 1 0 0 0 0 3 3 2 8 1 1 1 0 0 2 2 2 0 0 2 0 0 1
Nuclear Periphery 0 0 0 0 1 0 2 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 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 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 0 0 0 0 0
Vac/Vac Membrane 0 0 4 1 3 1 15 35 15 24 12 25 0 2 0 15 3 21 2 0 0 2 4 3
Unique Cell Count 102 265 259 196 314 307 289 544 372 259 332 362 168 253 289 256 290 191 102 262 246 125 140 192
Labelled Cell Count 103 271 259 198 325 311 298 564 395 270 360 378 170 255 292 272 300 203 102 262 246 125 140 192


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) 21.3 21.2 15.5 15.9 15.3 14.5 14.3 14.8 14.9 13.5 14.6 15.3 21.4 21.0 22.1 20.1 19.3 17.5 22.5 22.2 23.4
Std Deviation (1e-4) 4.2 3.3 3.5 3.2 2.8 3.0 3.1 3.6 3.8 4.9 4.2 4.6 3.3 3.4 3.5 5.8 5.4 6.2 4.7 4.2 4.4
Intensity Change (Log2) – – – 0.04 -0.02 -0.1 -0.12 -0.07 -0.06 -0.2 -0.09 -0.02 0.46 0.44 0.51 0.37 0.31 0.17 0.54 0.52 0.59


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 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
Bud Site 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cell Periphery 0 0 0 0 0 3.4 3.4 4.1 0 0 0 0 0 0 0
Cytoplasm 1.9 0.4 0.8 -3.9 -4.2 -5.6 -6.2 -5.8 -5.2 2.1 2.3 1.8 -1.2 1.8 -2.6
Endoplasmic Reticulum 0 0 0 1.2 1.9 2.7 1.4 1.9 1.7 0 0 0 0 0 0
Endosome 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
Mitochondria 0 0 0 3.0 0 4.6 3.7 5.7 4.1 0 0 0 0 0 0
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 0 0 0 0 0
Nucleolus 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
SpindlePole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Vacuole 0 0 0 2.3 3.0 1.8 3.9 1.5 3.1 0 0 0 2.6 0 4.3

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 14.2356 17.21 15.7399 14.3292 11.2199 15.4482 18.0469 22.1259 18.8725 17.9881 14.3984 18.7902 12.196 20.1706 18.4444 15.8042 18.8082 19.6009
Actin 0.005 0.0002 0.0095 0.0207 0.0626 0.0002 0.0078 0.0002 0.0006 0.0001 0.0223 0.0002 0.0016 0.0001 0.0001 0.0001 0 0.0001
Bud 0.0008 0.0002 0.0007 0.0002 0.0007 0.0001 0.0001 0.0001 0.0001 0 0.0004 0 0 0 0 0.0001 0 0
Bud Neck 0.0028 0.0002 0.0009 0.0004 0.003 0.0008 0.0002 0.0001 0.0002 0.0002 0.0008 0.0005 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003
Bud Periphery 0.0006 0 0.0009 0.0003 0.001 0 0 0 0 0 0.0005 0 0 0 0 0 0 0
Bud Site 0.0014 0.0002 0.009 0.0003 0.0034 0 0.0001 0.0001 0.0003 0 0.0008 0 0.0002 0 0 0 0 0
Cell Periphery 0.0001 0 0.0002 0.0001 0.0003 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.8382 0.9828 0.9033 0.8865 0.6854 0.945 0.961 0.9922 0.981 0.9895 0.7959 0.9826 0.7779 0.9972 0.9964 0.9963 0.998 0.9962
Cytoplasmic Foci 0.0321 0.001 0.016 0.0057 0.0366 0.007 0.0024 0.0006 0.0031 0.0003 0.0265 0.0014 0.0013 0.0001 0.0001 0.0003 0.0002 0.0002
Eisosomes 0.0001 0 0.0001 0.0002 0.0007 0 0.0001 0 0 0 0.0001 0 0 0 0 0 0 0
Endoplasmic Reticulum 0.0052 0.0006 0.0024 0.0072 0.0098 0.0024 0.0046 0.0005 0.0014 0.0005 0.0062 0.0026 0.0119 0 0.0001 0 0 0.0001
Endosome 0.024 0.0004 0.0149 0.0147 0.0764 0.007 0.0042 0.0002 0.0013 0.0001 0.0287 0.001 0.0063 0 0 0 0 0
Golgi 0.0051 0 0.0038 0.0047 0.0123 0.0003 0.0015 0 0.0008 0 0.0081 0.0001 0.0001 0 0 0 0 0
Lipid Particles 0.0119 0 0.0033 0.0138 0.0125 0.0004 0.0021 0 0.0007 0 0.0318 0 0.0002 0 0 0 0 0
Mitochondria 0.0066 0.0001 0.0034 0.0055 0.0098 0.0002 0.0004 0 0.0014 0 0.0034 0.0001 0.0006 0 0 0 0 0
None 0.0035 0.0007 0.0019 0.0077 0.0078 0.0006 0.0026 0.0006 0.0005 0.0004 0.004 0.0006 0.009 0.0005 0.0003 0.0007 0.0004 0.0003
Nuclear Periphery 0.0094 0.0016 0.0027 0.0065 0.0183 0.0038 0.0035 0.0007 0.0007 0.001 0.0138 0.0018 0.1026 0.0001 0.0001 0.0001 0 0.0002
Nucleolus 0.0005 0 0.0003 0.0002 0.0008 0 0 0 0 0 0.0005 0 0.0003 0 0 0 0 0
Nucleus 0.0324 0.0111 0.0145 0.0192 0.0112 0.0293 0.0067 0.004 0.0055 0.0076 0.0083 0.0086 0.0771 0.0017 0.0026 0.0019 0.0009 0.0024
Peroxisomes 0.0063 0 0.0045 0.0007 0.0094 0.0002 0.0006 0 0.0021 0 0.0253 0 0.0001 0 0 0 0 0
Punctate Nuclear 0.0107 0.0004 0.0031 0.0011 0.0236 0.0006 0.0012 0.0002 0.0001 0.0001 0.021 0.0002 0.0079 0 0 0 0 0.0001
Vacuole 0.0027 0.0004 0.0039 0.0032 0.0113 0.0016 0.0006 0.0001 0.0002 0.0002 0.0009 0.0002 0.0013 0 0 0 0 0
Vacuole Periphery 0.0008 0.0001 0.0007 0.0011 0.0033 0.0003 0.0002 0 0.0001 0 0.0006 0.0001 0.0013 0 0 0 0 0

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 45.3883 46.1708 35.2989 61.3066 49.7163 53.1844 51.9882 72.564 65.5386 57.0815
Translational Efficiency 2.7648 2.0259 2.6557 1.8649 1.7571 2.2322 2.1798 1.3731 1.8636 1.7947

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
535 978 2496 1023 1387 1658 1394 1646 1922 2636 3890 2669

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 1210.44 1655.46 1760.79 1950.24 1431.50 1511.17 1955.46 2243.41 1369.97 1564.70 1830.55 2131.04
Standard Deviation 234.16 299.77 342.80 451.91 565.14 280.40 340.75 447.51 505.53 296.06 354.58 471.27
Intensity Change Log 2 — 0.451701 0.540691 0.688120 — 0.078138 0.449980 0.648166 — 0.261351 0.492250 0.666609

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000454 0.000209 0.000046 0.001595 0.000176 0.000722 0.000168 0.001592 0.000254 0.000532 0.000090 0.001593
Bud Neck 0.000853 0.000531 0.000316 0.007646 0.000796 0.000526 0.000738 0.002344 0.000812 0.000528 0.000467 0.004377
Bud Site 0.019184 0.003256 0.000758 0.033961 0.003764 0.005370 0.002531 0.014602 0.008056 0.004586 0.001393 0.022022
Cell Periphery 0.000229 0.000087 0.000042 0.000209 0.000115 0.000101 0.000143 0.000164 0.000146 0.000096 0.000078 0.000181
Cytoplasm 0.879195* 0.875883* 0.810401* 0.591093* 0.865553* 0.890411* 0.829641* 0.826783* 0.869350* 0.885021* 0.817296* 0.736446*
Cytoplasmic Foci 0.048202 0.013044 0.002126 0.021628 0.014634 0.027097 0.006057 0.011685 0.023978 0.021883 0.003535 0.015496
Eisosomes 0.000004 0.000002 0.000001 0.000021 0.000003 0.000004 0.000002 0.000005 0.000003 0.000003 0.000001 0.000011
Endoplasmic Reticulum 0.001811 0.000288 0.000030 0.001648 0.000673 0.000577 0.000061 0.000119 0.000989 0.000470 0.000042 0.000705
Endosome 0.001106 0.000669 0.000041 0.022584 0.000631 0.002331 0.000412 0.004132 0.000763 0.001714 0.000174 0.011204
Golgi 0.002423 0.000749 0.000085 0.014390 0.000510 0.003683 0.003086 0.006292 0.001042 0.002595 0.001160 0.009396
Lipid Particles 0.000493 0.000450 0.000112 0.009644 0.000339 0.000950 0.000572 0.001590 0.000382 0.000764 0.000277 0.004677
Mitochondria 0.000247 0.000097 0.000081 0.012498 0.000227 0.000838 0.000092 0.001076 0.000233 0.000563 0.000085 0.005453
Mitotic Spindle 0.003744 0.004844 0.000741 0.089856 0.001077 0.007249 0.003885 0.019352 0.001819 0.006357 0.001868 0.046375
None 0.001434 0.009450 0.010613 0.004218 0.009578 0.005345 0.007495 0.006280 0.007311 0.006868 0.009496 0.005490
Nuclear Periphery 0.000054 0.000175 0.000056 0.001193 0.000089 0.000084 0.000097 0.000138 0.000080 0.000117 0.000071 0.000542
Nuclear Periphery Foci 0.002300 0.004365 0.000402 0.007506 0.003577 0.002634 0.001425 0.002695 0.003222 0.003276 0.000768 0.004539
Nucleolus 0.000067 0.000162 0.000078 0.003371 0.000299 0.000171 0.000080 0.000167 0.000234 0.000168 0.000079 0.001395
Nucleus 0.025741 0.073096 0.169301* 0.080188 0.082363 0.035886 0.132673* 0.077654 0.066602 0.049691 0.156175* 0.078625
Peroxisomes 0.000197 0.000209 0.000015 0.002137 0.000084 0.000597 0.000029 0.000995 0.000115 0.000453 0.000020 0.001433
Vacuole 0.009450 0.011368 0.004724 0.076832 0.014992 0.014470 0.010617 0.020356 0.013449 0.013319 0.006836 0.042003
Vacuole Periphery 0.002813 0.001065 0.000031 0.017783 0.000519 0.000955 0.000195 0.001980 0.001157 0.000996 0.000090 0.008038

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 2.36 5.32 -0.64 -1.94 -3.18 -1.11 -1.10 -2.22 -0.70 -2.11 -0.90 4.40 -2.43 -1.02 -3.02
Bud Neck 1.21 1.76 -9.09 -9.71 -9.89 1.87 -4.57 -4.48 -5.73 -1.39 2.18 -1.28 -9.55 -10.97 -9.33
Bud Site 5.95 7.08 1.78 -5.66 -7.46 -1.48 0.13 -4.67 -3.17 -5.32 3.57 7.11 -2.22 -6.16 -9.97
Cell Periphery 4.86 6.36 2.03 -4.82 -8.20 0.78 -3.79 -5.69 -3.43 1.16 2.29 0.89 -3.47 -4.48 -4.14
Cytoplasm 1.56 12.95 23.31 24.61 17.28 -3.43 12.31 10.36 14.47 -1.77 -2.23 17.38 22.67 26.51 10.63
Cytoplasmic Foci 8.28 11.75 9.04 1.35 -8.47 -6.72 1.60 -0.97 6.12 -2.76 0.47 12.49 6.07 6.08 -9.99
Eisosomes 3.34 6.11 -4.00 -6.10 -7.46 -0.87 0.90 -1.56 -0.06 -2.73 0.16 5.43 -4.21 -3.47 -8.89
Endoplasmic Reticulum 3.31 3.87 2.91 -1.34 -3.88 0.80 5.23 5.26 2.27 0.25 2.93 6.16 4.95 1.63 -3.90
Endosome 2.33 8.62 -4.51 -4.93 -5.66 -3.28 3.11 -2.07 1.28 -3.12 -2.78 8.42 -5.03 -2.76 -6.62
Golgi 5.28 8.12 -0.89 -3.13 -3.99 -3.38 -1.18 -2.45 1.17 -0.58 -2.35 1.66 -2.88 -0.35 -3.45
Lipid Particles -1.16 1.91 -4.08 -3.96 -4.23 -3.17 -8.05 -8.63 -4.90 -3.17 -3.46 -5.85 -7.07 -5.74 -6.04
Mitochondria 2.12 2.14 -2.16 -2.30 -2.30 -1.63 1.68 -0.83 1.13 -2.04 -1.29 2.28 -2.28 -1.64 -2.62
Mitotic Spindle -0.53 2.03 -6.28 -5.79 -6.86 -4.32 -2.82 -4.60 -0.13 -2.67 -4.14 -1.10 -7.88 -4.53 -7.57
None -7.83 -19.72 -4.54 6.05 16.08 3.68 2.83 4.08 0.49 4.05 0.95 -1.26 3.67 4.87 15.48
Nuclear Periphery -1.64 -4.17 -7.22 -4.32 -6.54 -0.13 -9.27 -6.11 -4.42 1.73 -1.42 -7.76 -8.49 -5.49 -6.51
Nuclear Periphery Foci -3.51 3.76 -1.97 1.48 -4.98 2.05 3.45 0.96 -0.95 -2.22 -0.82 6.95 -0.24 0.53 -6.51
Nucleolus -3.18 -2.04 -2.84 -2.56 -2.76 1.20 2.12 1.72 0.81 -2.49 0.82 2.08 -1.85 -2.36 -2.93
Nucleus -14.60 -43.33 -16.62 -3.53 21.20 12.51 -11.82 -0.67 -18.96 13.42 5.90 -27.35 -5.74 -16.31 26.46
Peroxisomes -0.29 6.66 -2.36 -1.79 -3.59 -3.28 3.49 -2.09 1.04 -2.46 -3.23 7.29 -3.19 0.04 -4.13
Vacuole -3.34 -2.02 -24.99 -23.98 -24.81 -3.04 -8.76 -16.03 -14.01 -8.25 -3.59 -4.69 -27.62 -26.17 -26.20
Vacuole Periphery 1.78 2.77 -0.73 -2.81 -3.89 -0.81 2.19 -0.39 0.42 -1.94 0.78 3.53 -1.39 -2.15 -4.38
Standard name
Human Ortholog
Description Endosomal Rab family GTPase; required for vacuolar protein sorting, endocytosis and multivesicular body (MVB) biogenesis and sorting; required for localization of the CORVET complex to endosomes; involved in autophagy and ionic stress tolerance; similar to Vps21p and Ypt53p; mammalian Rab5 homolog; protein abundance increases in response to DNA replication stress
Localization
Cell Percentages cytoplasm (97%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-7

Ypt52

Ypt52


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 (Ypt52-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