Standard name
Human Ortholog
Description Protein that may be involved in nonsense-mediated mRNA decay; interacts with Nam7p, relocalizes from nucleus to cytoplasmic foci upon 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 0.11 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
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
Bud Site 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 0.05 0 0 0 – 0 0 0 0 0 0 0 0.06 0.05 0.05 0 0 0 0 0 0
Cytoplasm 0.98 0.99 1.0 0.97 0.93 0.82 0.81 – 0.67 0.76 0.55 0.61 0.88 0.76 0.85 0.95 0.96 0.96 0.95 0.94 0.86 0.9 0.91 0.89
Endoplasmic Reticulum 0 0 0 0 0 0 0 – 0 0 0 0 0.05 0 0 0 0 0 0 0 0.05 0 0 0
Endosome 0 0 0 0 0 0 0 – 0 0 0 0 0.06 0.09 0.08 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
Mitochondria 0 0 0 0 0 0.1 0 – 0.24 0.15 0.35 0.33 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
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
Nucleolus 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
SpindlePole 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 0.1 0.12 0.17 – 0.13 0.11 0.14 0.11 0 0 0 0.06 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 1 0 0 0 0 0 0 – 0 2 1 0 6 36 8 0 0 0 0 1 1 1 0 1
Bud 1 2 0 0 0 0 1 – 1 0 4 0 1 7 2 0 0 0 0 1 0 0 0 2
Bud Neck 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
Bud Site 0 0 0 0 0 0 0 – 0 0 1 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 5 6 1 3 0 0 1 – 1 1 5 3 2 7 3 15 14 12 0 0 0 0 0 0
Cytoplasm 153 304 38 60 86 56 104 – 90 100 89 73 171 260 220 228 266 256 155 282 68 233 279 248
Endoplasmic Reticulum 2 3 0 1 0 0 2 – 4 4 2 0 9 12 10 9 8 9 1 1 3 10 8 6
Endosome 0 0 0 0 0 0 0 – 0 1 1 1 12 30 20 0 0 0 1 1 0 3 0 3
Golgi 1 0 0 0 1 0 2 – 0 0 0 0 2 15 3 2 2 0 0 0 0 0 3 1
Mitochondria 0 0 0 0 0 7 1 – 32 20 56 39 0 0 0 1 0 1 0 2 1 0 1 0
Nucleus 0 2 0 0 0 0 2 – 2 2 5 2 0 0 0 1 3 5 0 1 0 0 1 0
Nuclear Periphery 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 1
Nucleolus 0 0 0 0 0 0 0 – 0 0 1 1 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 0 0 0 0 0 0
SpindlePole 0 0 0 0 1 0 1 – 0 0 0 0 1 10 6 0 0 0 0 0 0 0 0 0
Vac/Vac Membrane 0 1 0 0 9 8 22 – 18 14 23 13 2 2 3 14 8 8 0 4 1 3 6 6
Unique Cell Count 156 307 38 62 92 68 128 134 132 162 119 195 340 259 241 276 266 164 301 79 260 306 278
Labelled Cell Count 163 318 39 64 97 71 136 148 144 188 132 206 379 276 270 301 291 164 301 79 260 306 278


Cytoplasm

(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) 13.1 12.3 12.7 12.0 13.5 7.7 9.5 – 8.0 8.6 7.5 7.6 13.6 14.0 14.1 17.6 18.5 18.3 11.4 12.2 13.0
Std Deviation (1e-4) 2.4 2.0 2.0 1.4 4.1 1.9 2.0 – 1.5 1.9 1.3 1.4 2.0 2.0 2.2 4.3 3.8 3.6 1.8 2.1 2.2
Intensity Change (Log2) – – – -0.08 0.08 -0.73 -0.43 – -0.67 -0.57 -0.76 -0.74 0.1 0.14 0.15 0.47 0.54 0.52 -0.15 -0.06 0.03


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
Bud 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
Bud Site 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
Cytoplasm -1.1 -1.6 -2.7 -2.9 – -4.1 -3.4 -5.2 -4.6 -2.3 -3.4 -2.6 -1.5 -1.2 -1.2
Endoplasmic Reticulum 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
Golgi 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
Mitochondria 0 0 0 0 – 3.3 0 4.3 4.1 0 0 0 0 0 0
Nucleus 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
Nucleolus 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
SpindlePole 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
Vacuole 0 0 0 2.7 – 0 0 0 0 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 6.5545 8.0813 7.3275 6.4079 6.4792 7.0319 7.4053 9.8864 8.7961 7.6917 7.7698 9.1072 12.3047 13.959 13.4194 12.6101 11.9188 13.2213
Actin 0.0087 0.0003 0.0033 0.0002 0.0002 0.0005 0.0262 0.0012 0.0215 0.0037 0.0319 0.0034 0.0042 0.0003 0.0004 0.0003 0.0002 0.0002
Bud 0.0003 0.0002 0.0002 0.0002 0.0009 0.0001 0.0005 0.0001 0.0002 0.0007 0.0016 0.0002 0.0001 0 0.0001 0.0001 0.0001 0
Bud Neck 0.0009 0.0001 0.0003 0.0003 0.0005 0.0007 0.0017 0.0002 0.0006 0.0025 0.0008 0.0014 0.0002 0.0001 0.0002 0.0003 0.0003 0.0006
Bud Periphery 0.0002 0.0001 0.0002 0 0.0001 0 0.0006 0 0 0.001 0.0018 0.0001 0 0 0 0 0 0
Bud Site 0.0008 0.0007 0.0005 0.0001 0.0015 0 0.0019 0.0002 0.0022 0.0007 0.0037 0.0001 0.0001 0.0001 0.0001 0.0001 0 0
Cell Periphery 0.0001 0.0002 0.0001 0 0.0001 0 0.0003 0.0001 0.0001 0.0002 0.0003 0 0 0 0 0 0 0
Cytoplasm 0.901 0.9836 0.9639 0.9746 0.9437 0.9638 0.8126 0.9872 0.9273 0.8707 0.7498 0.9438 0.9185 0.9907 0.9883 0.9696 0.9779 0.9807
Cytoplasmic Foci 0.0126 0.0024 0.0072 0.0039 0.0115 0.0054 0.0245 0.0024 0.0184 0.0336 0.0245 0.0072 0.0134 0.0019 0.0021 0.0068 0.0032 0.0034
Eisosomes 0.0002 0 0.0001 0 0 0 0.0002 0 0.0001 0.0001 0.0002 0 0 0 0 0 0 0
Endoplasmic Reticulum 0.0169 0.0033 0.0036 0.0032 0.0022 0.0082 0.0142 0.0029 0.0059 0.0031 0.01 0.0109 0.0156 0.0022 0.0034 0.0018 0.0074 0.0055
Endosome 0.0226 0.0018 0.0088 0.007 0.0194 0.0103 0.0227 0.0015 0.0069 0.0332 0.0622 0.0177 0.0065 0.0013 0.0014 0.014 0.0027 0.0038
Golgi 0.0024 0.0002 0.001 0.0002 0.0003 0.0007 0.01 0.0002 0.0019 0.006 0.036 0.0028 0.0011 0.0005 0.0001 0.0015 0.0001 0.0001
Lipid Particles 0.0021 0.0001 0.0004 0 0 0.0005 0.0125 0 0.0025 0.0007 0.0132 0.0008 0.0039 0 0 0 0 0
Mitochondria 0.0027 0.0001 0.0009 0.0002 0.0002 0.0006 0.0047 0.0001 0.0004 0.0329 0.039 0.0008 0.0004 0.0001 0.0001 0.0002 0.0001 0.0002
None 0.0081 0.001 0.0039 0.0014 0.0084 0.0009 0.0077 0.0013 0.0032 0.002 0.0033 0.001 0.0071 0.0006 0.0011 0.0011 0.0028 0.001
Nuclear Periphery 0.0062 0.0014 0.0013 0.002 0.0014 0.0031 0.0109 0.0008 0.0016 0.001 0.0048 0.0051 0.0055 0.0006 0.0007 0.0008 0.0015 0.0016
Nucleolus 0.0017 0 0.0001 0 0.0001 0 0.0009 0 0.0001 0.0001 0.0003 0 0.0001 0 0 0 0 0
Nucleus 0.0046 0.0033 0.0017 0.0035 0.0035 0.0029 0.0164 0.0012 0.0022 0.0016 0.0025 0.0021 0.0051 0.0012 0.0013 0.0018 0.0027 0.0022
Peroxisomes 0.0011 0 0.0004 0 0.0001 0.0001 0.0107 0 0.0031 0.0021 0.0061 0.0002 0.0094 0 0 0 0 0
Punctate Nuclear 0.0037 0.0001 0.0006 0.0003 0.0012 0.0003 0.0091 0.0002 0.0006 0.0007 0.0021 0.0004 0.0043 0.0001 0.0001 0.0001 0.0001 0.0001
Vacuole 0.0023 0.0007 0.0011 0.0023 0.0036 0.0013 0.0093 0.0003 0.0009 0.0023 0.0036 0.0012 0.0023 0.0002 0.0004 0.001 0.0006 0.0005
Vacuole Periphery 0.0007 0.0002 0.0004 0.0005 0.0011 0.0005 0.0027 0.0001 0.0002 0.0009 0.0025 0.0006 0.0023 0 0.0001 0.0003 0.0001 0.0002

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 15.1151 22.52 16.7108 19.3887 14.1537 10.0712 20.1135 22.0277 19.5204 24.1972
Translational Efficiency 1.6358 1.0432 1.2616 1.4612 1.5663 2.6364 1.5015 1.3666 1.6602 1.4106

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
109 1347 1525 1650 1973 107 1688 2267 2082 1454 3213 3917

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 1126.87 1177.58 1554.44 1642.33 1049.63 1240.38 1501.43 1754.99 1053.67 1182.20 1526.59 1707.53
Standard Deviation 179.22 189.54 229.92 288.84 144.35 132.98 208.16 280.12 147.39 186.69 220.36 289.23
Intensity Change Log 2 — 0.063504 0.464074 0.543423 — 0.240901 0.516456 0.741582 — 0.151780 0.489573 0.642387

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.001885 0.000783 0.000248 0.000878 0.000612 0.000810 0.000322 0.000484 0.000678 0.000785 0.000287 0.000650
Bud Neck 0.001604 0.001137 0.001113 0.001861 0.001460 0.001773 0.001061 0.001461 0.001467 0.001184 0.001086 0.001629
Bud Site 0.057621 0.028871 0.004674 0.020591 0.019372 0.033223 0.009986 0.013949 0.021375 0.029192 0.007465 0.016747
Cell Periphery 0.000583 0.000151 0.000087 0.000486 0.000156 0.000194 0.000166 0.000140 0.000179 0.000155 0.000128 0.000286
Cytoplasm 0.367328* 0.748714* 0.883358* 0.849732* 0.652367* 0.507015* 0.883428* 0.882515* 0.637445* 0.730928* 0.883395* 0.868705*
Cytoplasmic Foci 0.422771* 0.141775 0.015638 0.029469 0.231005* 0.288151* 0.030886 0.024214 0.241045* 0.152546 0.023649 0.026428
Eisosomes 0.000069 0.000010 0.000002 0.000004 0.000025 0.000032 0.000003 0.000003 0.000027 0.000012 0.000002 0.000004
Endoplasmic Reticulum 0.022969 0.003098 0.000620 0.000456 0.008728 0.005598 0.000572 0.000222 0.009474 0.003282 0.000595 0.000320
Endosome 0.022000 0.009129 0.002301 0.002834 0.011316 0.039770 0.003511 0.002760 0.011876 0.011384 0.002937 0.002792
Golgi 0.028715 0.014601 0.001704 0.006391 0.017840 0.012324 0.004045 0.003225 0.018409 0.014434 0.002934 0.004558
Lipid Particles 0.008548 0.002551 0.001497 0.007211 0.002819 0.005473 0.003559 0.003811 0.003119 0.002766 0.002581 0.005243
Mitochondria 0.001384 0.000636 0.000079 0.000290 0.002236 0.000195 0.000042 0.000199 0.002192 0.000603 0.000060 0.000237
Mitotic Spindle 0.002291 0.002635 0.013460 0.007597 0.001637 0.000952 0.004182 0.006625 0.001672 0.002512 0.008586 0.007035
None 0.000094 0.000900 0.001811 0.000968 0.000959 0.000095 0.000664 0.000878 0.000914 0.000841 0.001208 0.000916
Nuclear Periphery 0.000583 0.000080 0.000263 0.000068 0.000127 0.000066 0.000059 0.000060 0.000151 0.000079 0.000156 0.000063
Nuclear Periphery Foci 0.004168 0.002574 0.004573 0.003894 0.000806 0.002659 0.004404 0.002116 0.000982 0.002581 0.004484 0.002865
Nucleolus 0.000319 0.000174 0.000116 0.000155 0.000120 0.000069 0.000102 0.000199 0.000131 0.000166 0.000109 0.000181
Nucleus 0.006101 0.006587 0.043308 0.013616 0.007784 0.005195 0.011089 0.013933 0.007696 0.006485 0.026382 0.013799
Peroxisomes 0.002107 0.001927 0.000072 0.001263 0.000916 0.002862 0.000238 0.000738 0.000978 0.001996 0.000159 0.000959
Vacuole 0.033422 0.028976 0.024433 0.049167 0.032964 0.090972 0.040638 0.041517 0.032988 0.033539 0.032947 0.044739
Vacuole Periphery 0.015437 0.004688 0.000642 0.003069 0.006750 0.002575 0.001042 0.000950 0.007205 0.004532 0.000852 0.001843

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 2.58 3.82 1.81 -0.81 -2.76 -0.81 1.09 -0.40 0.49 -1.45 -0.75 2.37 -0.82 -0.19 -3.12
Bud Neck 1.35 -0.38 -2.41 -7.81 -3.57 -1.01 0.73 -4.12 -1.48 -5.27 1.79 -0.51 -5.60 -8.47 -6.04
Bud Site 4.30 8.12 5.63 3.42 -9.97 -2.30 6.48 2.66 3.01 -3.78 -3.57 10.36 2.64 5.76 -9.79
Cell Periphery 4.58 5.06 1.24 -2.53 -2.97 -1.01 -0.82 0.99 1.33 1.55 1.91 3.25 -1.75 -2.31 -2.65
Cytoplasm -13.50 -17.51 -16.07 -7.42 5.66 5.20 -29.65 -26.70 -12.28 3.63 -9.90 -32.89 -28.46 -13.10 6.23
Cytoplasmic Foci 11.69 17.18 16.59 22.12 -7.97 -2.87 40.84 41.87 13.44 2.30 13.28 45.30 44.25 25.39 -3.00
Eisosomes 4.33 4.88 4.72 5.24 -5.16 -0.86 11.82 11.05 3.59 -1.91 7.13 12.80 11.90 6.83 -4.42
Endoplasmic Reticulum 2.98 3.36 3.39 5.83 1.80 1.15 7.88 8.20 2.06 3.66 5.43 8.50 8.79 6.44 3.80
Endosome 4.31 6.68 6.63 8.89 -0.51 -4.45 12.57 13.42 5.81 1.72 0.48 14.85 15.23 10.27 1.03
Golgi 3.98 7.84 6.79 8.88 -4.35 1.15 18.64 19.13 1.95 1.83 3.74 22.49 19.36 11.47 -1.98
Lipid Particles 1.71 1.86 0.09 -7.81 -8.80 -1.04 -3.90 -5.82 0.05 -2.00 0.92 -0.27 -7.82 -8.03 -8.01
Mitochondria 1.61 3.34 2.94 1.58 -1.46 3.25 3.55 3.35 0.24 -3.68 2.50 3.63 3.42 1.76 -2.93
Mitotic Spindle -0.45 -7.23 -4.20 -4.21 2.61 1.54 -3.77 -5.78 -6.54 -2.41 -1.75 -8.52 -7.33 -6.29 0.83
None -3.84 -14.28 -5.75 0.04 5.04 5.52 1.78 0.49 -12.50 -2.38 0.32 -1.69 0.21 -0.22 3.25
Nuclear Periphery 1.21 0.50 1.16 -1.20 10.16 0.80 0.62 0.27 -2.58 -3.67 0.92 -0.75 0.60 -1.65 8.27
Nuclear Periphery Foci 0.88 -0.54 -0.07 -4.66 1.95 -2.42 -12.61 -8.10 -0.52 5.50 -4.80 -14.30 -10.96 -3.06 5.43
Nucleolus 0.66 0.80 0.67 0.02 -1.22 4.10 0.94 -8.90 -10.86 -9.92 -1.00 0.13 -4.84 -1.20 -6.70
Nucleus -0.17 -13.82 -3.99 -9.31 16.70 2.77 -9.82 -13.75 -12.05 -5.59 1.74 -25.24 -15.07 -14.79 11.90
Peroxisomes 0.34 5.37 2.05 1.75 -4.02 -1.75 6.92 0.97 1.87 -5.66 -2.98 8.85 0.18 2.97 -6.16
Vacuole 0.55 -1.25 -5.95 -13.79 -9.28 -4.86 -6.84 -11.63 2.29 -4.27 -0.59 -6.48 -16.19 -12.89 -9.51
Vacuole Periphery 2.36 3.30 2.92 3.04 -3.64 6.29 10.88 11.13 4.31 1.33 3.24 11.54 9.88 4.80 -3.17
Standard name
Human Ortholog
Description Protein that may be involved in nonsense-mediated mRNA decay; interacts with Nam7p, relocalizes from nucleus to cytoplasmic foci upon DNA replication stress
Localization
Cell Percentages cytoplasm (99%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-5

Nmd4

Nmd4


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 (Nmd4-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