Standard name
Human Ortholog
Description Subunit of the membrane-associated retromer complex; endosomal protein; essential for endosome-to-Golgi retrograde transport; forms a subcomplex with Vps35p and Vps26p that selects cargo proteins for endosome-to-Golgi retrieval
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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 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 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.93 0.96 0.97 0.97 0.91 0.89 0.82 0.84 0.73 0.73 0.61 0.64 0.98 0.99 0.98 0.39 0.36 0.28 0.83 0.78 0.82 0.8 0.82 0.8
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0
Endosome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.38 0.39 0.44 0 0 0.05 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 0.06 0.05 0.06 0.07 0.1 0.22 0.25 0.16 0.38 0.32 0.49 0.49 0 0 0 0.13 0.07 0.08 0.06 0.1 0.07 0.06 0.05 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 0.17 0.16 0.23 0 0 0 0 0 0
Vac/Vac Membrane 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.19 0.27 0.29 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 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 3 1 5 1 5
Bud 0 1 0 0 7 6 3 3 4 1 2 1 0 0 0 2 3 2 1 2 0 5 4 12
Bud Neck 0 0 0 0 0 0 0 2 2 1 0 0 4 0 1 3 0 0 1 1 0 0 0 2
Bud Site 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 1 1 0 0 3 0 1 4 0 2 1 0 1 2 1 0 0 0 0 1 0 0 0 2
Cytoplasm 93 248 75 209 333 268 280 363 140 181 76 86 183 325 362 51 49 40 87 199 79 116 218 278
Endoplasmic Reticulum 0 1 1 0 2 1 1 0 2 0 2 0 3 3 0 5 8 4 0 1 0 0 4 1
Endosome 1 0 1 0 5 1 1 6 1 6 3 1 0 0 3 50 52 63 2 4 4 1 3 1
Golgi 1 0 0 0 1 0 0 1 0 0 0 0 0 0 1 2 0 1 2 2 1 2 3 0
Mitochondria 6 12 5 15 35 66 87 69 74 80 61 65 0 0 0 17 9 12 6 26 6 8 13 14
Nucleus 0 3 0 1 1 2 1 3 4 4 4 0 0 0 1 0 1 3 0 0 0 0 0 1
Nuclear Periphery 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 1
Nucleolus 1 0 0 1 2 0 0 0 2 1 2 0 0 0 0 2 1 2 0 0 0 0 0 0
Peroxisomes 0 0 0 0 1 0 0 4 2 3 0 1 0 0 0 1 0 5 0 0 0 0 0 0
SpindlePole 0 0 0 0 1 1 2 2 5 3 3 1 1 0 0 22 22 33 1 1 0 0 2 3
Vac/Vac Membrane 0 0 0 1 5 3 2 8 0 8 3 3 0 2 2 25 36 41 0 8 0 3 6 12
Unique Cell Count 100 259 77 216 364 301 343 432 193 249 124 134 187 328 368 131 135 142 105 256 97 146 266 346
Labelled Cell Count 103 267 82 227 396 348 378 465 237 290 158 158 192 332 371 182 185 208 105 256 97 146 266 346


Ambiguous

(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) 3.4 3.9 3.7 3.8 4.2 3.8 3.5 4.6 4.1 4.2 4.6 4.3 4.9 4.8 5.1 5.9 5.9 6.2 5.6 5.6 5.7
Std Deviation (1e-4) 0.6 0.8 1.6 2.2 2.5 2.2 2.1 3.1 2.2 2.5 2.8 2.8 1.1 1.4 1.4 1.2 1.2 1.4 1.6 2.1 2.5
Intensity Change (Log2) – – – 0.05 0.17 0.04 -0.08 0.31 0.14 0.2 0.33 0.23 0.41 0.38 0.47 0.67 0.68 0.76 0.6 0.6 0.62


Localization RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3
Actin – – – – – – – – – – – – – – –
Bud – – – – – – – – – – – – 0 0 0
Bud Neck – – – – – – – – – – – – 0 0 0
Bud Site – – – – – – – – – – – – 0 0 0
Cell Periphery – – – – – – – – – – – – 0 0 0
Cyto – – – – – – – – – – – – – – –
Endoplasmic Reticulum – – – – – – – – – – – – 0 0 0
Endosome – – – – – – – – – – – – 0 0 0
Golgi – – – – – – – – – – – – 0 0 0
Mitochondria – – – – – – – – – – – – 0 0 0
Nuclear Periphery – – – – – – – – – – – – 0 0 0
Nuc – – – – – – – – – – – – – – –
Nucleolus – – – – – – – – – – – – 0 0 0
Peroxisomes – – – – – – – – – – – – 0 0 0
SpindlePole – – – – – – – – – – – – 0 0 0
Vac – – – – – – – – – – – – – – –
Cortical Patches – – – – – – – – – – – – 0 0 0
Cytoplasm – – – – – – – – – – – – 0 0 0
Nucleus – – – – – – – – – – – – 0 0 0
Vacuole – – – – – – – – – – – – 4.1 5.0 5.2

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 1.758 0.6348 0.7967 0.3506 0.082 0.3565 0.8924 -0.2592 0.1846 -0.1573 -0.9689 -0.0766 -2.1809 -1.8208 -1.9976 -1.9717 -2.0199 -2.0271
Actin 0.0412 0.0034 0.0133 0.0197 0.009 0.0034 0.0897 0.0014 0.0234 0.0001 0 0.0008 0.0476 0.0002 0.0054 0.0002 0.0001 0.0004
Bud 0.0069 0.0268 0.0099 0.0083 0.0188 0.0086 0.0009 0.0008 0.0129 0 0 0.0001 0.0002 0.0001 0.0006 0.0001 0.0001 0
Bud Neck 0.0167 0.0037 0.0128 0.0014 0.0018 0.0155 0.0024 0.0003 0.0008 0.0001 0 0.0005 0.0007 0.0001 0.0005 0.0033 0.0001 0.0004
Bud Periphery 0.0096 0.0089 0.0065 0.0106 0.0143 0.0072 0.0013 0.0009 0.0024 0.0001 0 0.0001 0.0002 0.0001 0.001 0 0.0001 0.0001
Bud Site 0.0515 0.0296 0.0326 0.005 0.0253 0.0023 0.0057 0.0106 0.0109 0.0001 0 0.0009 0.0005 0.0003 0.0016 0.0001 0.0001 0.0001
Cell Periphery 0.0017 0.0009 0.0008 0.0026 0.0025 0.0006 0.0013 0.0002 0.0003 0.0001 0.0001 0.0001 0.0001 0.0002 0.0002 0 0.0001 0.0001
Cytoplasm 0.0479 0.0881 0.0722 0.093 0.0672 0.1121 0.0577 0.0239 0.0227 0.0495 0.0201 0.0804 0.0342 0.1503 0.1726 0.0891 0.1745 0.1926
Cytoplasmic Foci 0.0549 0.0307 0.0416 0.0234 0.0553 0.0332 0.036 0.0051 0.0181 0.0067 0.0022 0.0185 0.0227 0.0072 0.0288 0.0372 0.0139 0.012
Eisosomes 0.0011 0.0003 0.0004 0.0003 0.0003 0.0001 0.0011 0.0003 0.0007 0.0002 0.0002 0.0002 0.0005 0.0002 0.0002 0.0002 0 0.0001
Endoplasmic Reticulum 0.0092 0.0014 0.001 0.0013 0.0025 0.0012 0.0304 0.0009 0.0006 0.0014 0.0006 0.0008 0.0012 0.0025 0.0031 0.0013 0.0016 0.0014
Endosome 0.0432 0.0025 0.0124 0.0186 0.0155 0.0087 0.0513 0.0018 0.007 0.0048 0.0011 0.0069 0.0059 0.0038 0.0151 0.0107 0.0088 0.0101
Golgi 0.0136 0.0003 0.0072 0.0142 0.0211 0.0024 0.0212 0.0001 0.0042 0.0001 0.0001 0.0029 0.0047 0.0002 0.0034 0.0003 0.0002 0.0009
Lipid Particles 0.0302 0.0008 0.0098 0.0111 0.0078 0.0045 0.0278 0.0006 0.0021 0.0011 0.0008 0.0119 0.0348 0.0007 0.0022 0.0012 0.0005 0.0011
Mitochondria 0.0483 0.0086 0.0145 0.0208 0.0255 0.0066 0.0058 0.0004 0.0019 0.0005 0.0002 0.0023 0.0016 0.0005 0.0035 0.0004 0.0003 0.0054
None 0.5191 0.7408 0.7008 0.7305 0.6647 0.7359 0.5904 0.9493 0.8866 0.9292 0.9725 0.867 0.8216 0.828 0.732 0.8283 0.7893 0.7662
Nuclear Periphery 0.0181 0.0017 0.0018 0.0026 0.0027 0.0021 0.0199 0.0004 0.0004 0.0009 0.0004 0.0007 0.0015 0.0009 0.0038 0.0015 0.0008 0.0007
Nucleolus 0.0114 0.0059 0.0082 0.0024 0.0147 0.0034 0.0012 0.0004 0.0006 0.0002 0.0001 0.0002 0.0007 0.0002 0.0005 0.0006 0.0001 0.0003
Nucleus 0.0118 0.0195 0.0094 0.0041 0.0104 0.0097 0.0054 0.0007 0.0016 0.0006 0.0002 0.0017 0.0006 0.001 0.0034 0.002 0.0009 0.0012
Peroxisomes 0.0372 0.0048 0.0175 0.0061 0.0151 0.0039 0.0383 0.0002 0.0007 0.0001 0 0.002 0.0145 0.0002 0.0049 0.0005 0.0002 0.0011
Punctate Nuclear 0.0114 0.0165 0.0209 0.0164 0.0151 0.0329 0.0077 0.0007 0.0012 0.0005 0.0001 0.0009 0.0053 0.0007 0.0054 0.0142 0.0009 0.0018
Vacuole 0.0112 0.004 0.0054 0.0066 0.0065 0.0049 0.0031 0.0008 0.0008 0.0032 0.0012 0.001 0.0007 0.0023 0.0099 0.0074 0.0066 0.0037
Vacuole Periphery 0.004 0.0007 0.0011 0.001 0.0041 0.0009 0.0015 0.0001 0.0001 0.0005 0.0001 0.0003 0.0003 0.0003 0.0021 0.0014 0.0007 0.0005

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 22.7439 24.398 29.3118 33.7443 26.1184 7.7936 29.0739 36.0745 39.3166 33.6497
Translational Efficiency 2.0325 1.7286 1.3691 1.5162 1.4055 6.8224 1.7419 1.2192 1.3837 1.4236

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
2091 1942 2981 1097 1269 106 52 1441 3360 2048 3033 2538

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 558.23 603.73 710.89 778.02 616.61 650.57 959.23 776.40 580.28 606.15 715.15 777.10
Standard Deviation 66.71 90.43 89.11 138.36 65.99 93.70 208.00 124.04 72.22 91.20 97.91 130.43
Intensity Change Log 2 — 0.113044 0.348767 0.478948 — 0.077346 0.637518 0.332442 — 0.094418 0.507487 0.403912

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000194 0.000151 0.000151 0.003902 0.000193 0.000475 0.034929 0.000823 0.000194 0.000168 0.000747 0.002154
Bud Neck 0.031095 0.032732 0.017019 0.010827 0.020592 0.039236 0.005647 0.012944 0.027128 0.033069 0.016824 0.012029
Bud Site 0.005545 0.008894 0.015529 0.064037 0.003410 0.021789 0.133717* 0.037113 0.004739 0.009561 0.017555 0.048751
Cell Periphery 0.000246 0.000129 0.000157 0.000282 0.000216 0.000325 0.002537 0.000268 0.000235 0.000139 0.000198 0.000274
Cytoplasm 0.417886* 0.431280* 0.394696* 0.403697* 0.418150* 0.243151* 0.223098* 0.471645* 0.417985* 0.421543* 0.391754* 0.442276*
Cytoplasmic Foci 0.248238* 0.195869* 0.006801 0.019186 0.322663* 0.379455* 0.080487 0.036867 0.276347* 0.205371* 0.008064 0.029225
Eisosomes 0.000401 0.000142 0.000016 0.000062 0.000379 0.000323 0.000286 0.000066 0.000393 0.000151 0.000021 0.000065
Endoplasmic Reticulum 0.001365 0.000743 0.001521 0.002761 0.001106 0.000352 0.016781 0.001448 0.001267 0.000723 0.001783 0.002016
Endosome 0.009690 0.009409 0.001228 0.010856 0.016132 0.036062 0.057949 0.012019 0.012123 0.010789 0.002201 0.011516
Golgi 0.006240 0.003591 0.000126 0.006267 0.007133 0.012291 0.068698 0.009768 0.006577 0.004041 0.001302 0.008255
Lipid Particles 0.018781 0.008657 0.000476 0.001829 0.016715 0.015990 0.006318 0.003529 0.018001 0.009037 0.000577 0.002794
Mitochondria 0.013836 0.018689 0.002362 0.002190 0.008960 0.013668 0.011493 0.005944 0.011995 0.018430 0.002519 0.004321
Mitotic Spindle 0.001086 0.002916 0.011853 0.047796 0.001432 0.006720 0.030878 0.026741 0.001217 0.003113 0.012179 0.035842
None 0.008998 0.009920 0.004298 0.008176 0.001525 0.001262 0.001934 0.007658 0.006176 0.009472 0.004257 0.007882
Nuclear Periphery 0.000388 0.000686 0.001738 0.001845 0.000861 0.000447 0.000947 0.001421 0.000567 0.000673 0.001724 0.001604
Nuclear Periphery Foci 0.000224 0.000206 0.000199 0.001376 0.000258 0.000211 0.002695 0.000851 0.000237 0.000206 0.000241 0.001078
Nucleolus 0.002445 0.002144 0.000589 0.000704 0.000974 0.001689 0.002689 0.000851 0.001890 0.002120 0.000625 0.000787
Nucleus 0.193008* 0.220127* 0.523577* 0.314138* 0.120228 0.117522 0.099927 0.282253* 0.165521* 0.214816* 0.516313* 0.296035*
Peroxisomes 0.009121 0.007684 0.000450 0.000953 0.010121 0.052840 0.006923 0.002301 0.009498 0.010021 0.000561 0.001718
Vacuole 0.030075 0.044348 0.016819 0.095874 0.047500 0.055101 0.202786* 0.082808 0.036656 0.044905 0.020007 0.088455
Vacuole Periphery 0.001138 0.001685 0.000395 0.003242 0.001450 0.001090 0.009283 0.002681 0.001256 0.001654 0.000548 0.002924

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 0.86 0.37 -2.64 -2.73 -2.68 -2.16 -2.55 -4.65 -1.29 2.51 0.62 -2.28 -3.68 -3.83 -1.45
Bud Neck -0.60 7.34 11.84 10.82 4.46 -1.88 8.67 4.81 3.01 -4.17 -2.67 6.36 12.11 11.23 4.28
Bud Site -3.11 -6.49 -6.94 -5.86 -3.97 -2.18 -3.63 -7.64 -0.25 2.93 -4.57 -7.98 -10.09 -7.21 -3.67
Cell Periphery 7.80 4.57 3.59 -4.89 -1.84 -0.76 -1.61 0.61 0.88 1.62 6.69 2.22 2.86 -4.76 -0.67
Cytoplasm -1.50 5.50 12.71 13.43 8.58 7.55 4.80 3.57 -5.91 -3.76 -0.35 6.51 10.47 9.32 4.01
Cytoplasmic Foci 8.02 51.68 50.20 39.11 -3.75 -2.03 16.41 44.53 14.64 2.31 11.84 69.33 64.84 39.00 -10.00
Eisosomes 10.08 15.59 13.02 7.46 -20.61 1.22 2.08 7.75 7.03 3.07 10.74 17.45 14.80 9.25 -24.24
Endoplasmic Reticulum 2.48 -2.32 -11.10 -14.74 -11.02 2.63 -3.14 -6.48 -14.21 2.73 2.80 -4.17 -12.29 -18.51 -9.24
Endosome 0.45 13.42 5.78 5.52 -5.17 -2.19 -2.39 7.33 3.36 3.32 1.67 17.23 8.38 5.60 -6.27
Golgi 4.18 12.90 6.18 2.51 -2.89 -0.67 -1.93 1.91 1.14 2.08 3.72 9.55 4.13 0.90 -2.98
Lipid Particles 8.88 18.58 16.79 10.62 -12.76 0.25 5.61 12.16 3.79 2.18 9.62 23.68 20.08 10.12 -7.49
Mitochondria -2.34 10.13 10.98 10.44 1.56 -0.69 0.34 3.78 1.78 1.50 -3.48 10.66 9.93 9.75 -0.38
Mitotic Spindle -2.21 -6.88 -9.08 -8.51 -6.11 -1.25 -1.48 -7.16 -1.15 0.25 -2.42 -6.96 -11.65 -10.21 -5.95
None -0.42 4.89 2.34 2.22 -3.83 0.78 -0.42 -6.36 -6.28 -3.95 -2.11 3.26 0.29 2.37 -4.02
Nuclear Periphery -1.82 -21.83 -19.79 -14.73 -11.59 1.15 -1.88 -6.23 -15.45 -2.61 -0.61 -11.28 -19.27 -15.19 -11.72
Nuclear Periphery Foci 0.42 -1.33 -8.59 -8.67 -8.34 0.12 -3.73 -8.64 -8.14 2.97 0.79 -2.61 -11.79 -12.03 -10.47
Nucleolus 0.48 6.34 5.09 3.41 -2.69 -1.81 -1.13 1.96 2.51 1.38 -0.73 6.71 5.64 3.82 -2.69
Nucleus -4.35 -50.26 -18.79 -15.13 16.46 0.00 -1.05 -26.78 -12.06 -6.98 -8.78 -58.07 -30.00 -18.92 22.38
Peroxisomes 1.59 12.76 12.78 13.00 0.03 -4.14 3.05 10.01 5.11 2.30 -0.39 16.67 15.78 11.93 -2.53
Vacuole -6.78 3.63 -24.30 -21.91 -25.34 -1.58 -5.73 -18.72 -7.24 2.45 -4.64 5.04 -31.10 -27.70 -32.73
Vacuole Periphery -3.03 6.06 0.35 1.72 -1.81 1.38 -1.33 0.43 -0.50 1.38 -2.17 5.30 0.36 1.57 -2.36
Standard name
Human Ortholog
Description Subunit of the membrane-associated retromer complex; endosomal protein; essential for endosome-to-Golgi retrograde transport; forms a subcomplex with Vps35p and Vps26p that selects cargo proteins for endosome-to-Golgi retrieval
Localization
Cell Percentages —
Cell Cycle Regulation No
Subcompartmental Group N/A

Vps29

Vps29


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 (Vps29-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