Standard name
Human Ortholog
Description Defining member of the SET3 histone deacetylase complex; which is a meiosis-specific repressor of sporulation genes; necessary for efficient transcription by RNAPII; one of two yeast proteins that contains both SET and PHD domains; SET3 has a paralog, SET4, 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
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 0.06 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
Cytoplasm 0 0 0 0 0 0.05 0 – 0 0 0 0 0 0.09 0.12 0.06 0.06 0.08 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 0 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 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 0.15 0.3 0 0.08 0.05 0.19 0.2 – 0.44 0.41 0.4 0.27 0.13 0.07 0.05 0.05 0 0.1 0 0 0 0 0 0
Nucleus 0.81 0.86 0.96 0.96 0.9 0.85 0.85 – 0.73 0.68 0.69 0.71 0.89 0.83 0.79 0.84 0.85 0.82 0.71 0.76 0.77 0.65 0.66 0.6
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 0.34 0.17 0 0.05 0.05 0.09 0.12 – 0.25 0.27 0.33 0.25 0.22 0.16 0.2 0.08 0.09 0.07 0.22 0.13 0.17 0.21 0.22 0.22
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 0.07 0 0 0 0 – 0 0 0 0 0 0 0 0.05 0.05 0.06 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 0 0 0 0 0.06 0.06 0.08
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
Bud 0 2 0 1 2 1 3 – 0 4 6 3 0 0 0 2 0 0 1 1 0 3 5 12
Bud Neck 0 0 2 1 1 0 1 – 0 2 4 4 0 0 0 0 0 0 0 1 1 1 1 7
Bud Site 0 0 1 0 5 6 5 – 10 16 16 22 0 0 1 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
Cytoplasm 4 4 2 4 16 16 15 – 4 12 9 12 14 50 74 14 12 8 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 1 1 0 0 – 0 0 0 0 0 0 0 2 3 1 0 0 0 1 0 2
Endosome 0 1 0 0 1 0 1 – 0 0 0 0 1 3 2 4 3 1 2 3 3 3 5 6
Golgi 0 0 0 0 0 0 0 – 0 0 0 0 0 0 2 1 2 0 1 4 0 3 2 0
Mitochondria 25 85 11 19 17 67 93 – 127 152 160 108 62 37 32 12 4 10 2 5 1 1 3 7
Nucleus 132 244 278 229 330 294 396 – 211 252 276 286 438 460 468 201 163 80 116 225 236 237 321 375
Nuclear Periphery 0 0 0 0 0 1 2 – 3 2 1 3 0 5 4 5 0 0 0 0 0 0 1 0
Nucleolus 56 47 12 12 18 32 56 – 73 99 132 99 108 91 119 18 17 7 35 38 50 77 109 140
Peroxisomes 0 0 0 0 0 0 0 – 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0
SpindlePole 1 6 21 4 13 9 16 – 3 8 6 18 4 4 2 13 9 6 1 2 2 7 7 15
Vac/Vac Membrane 0 2 3 0 2 1 1 – 0 2 0 1 1 3 1 7 7 1 1 11 7 21 27 52
Unique Cell Count 163 284 291 238 368 345 464 291 369 398 400 491 556 593 239 191 97 165 297 306 364 490 630
Labelled Cell Count 218 391 330 271 406 427 589 431 549 610 556 628 654 706 279 221 114 165 297 306 364 490 630


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) 6.0 5.1 6.0 5.5 6.1 4.9 5.0 – 4.5 4.3 4.3 4.8 5.6 5.6 5.6 7.4 8.0 6.9 5.3 5.4 5.8
Std Deviation (1e-4) 1.0 0.9 0.9 0.8 1.5 1.3 1.3 – 1.0 0.9 1.1 1.0 1.0 1.2 1.5 1.7 1.7 1.5 1.1 1.1 1.3
Intensity Change (Log2) – – – -0.13 0.02 -0.3 -0.26 – -0.42 -0.49 -0.5 -0.34 -0.1 -0.11 -0.1 0.29 0.41 0.19 -0.2 -0.16 -0.06


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 0 2.9 3.0 2.3 – 0 2.3 0 2.1 2.1 4.8 5.9 3.5 3.6 0
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 2.1 0.5 6.0 6.3 – 0 0 0 0 4.1 1.7 1.0 0.7 -1.0 2.5
Nucleus 0.4 -2.8 -4.3 -4.4 – -7.6 -8.7 -8.6 -8.1 -3.1 -5.3 -6.4 -4.4 -3.9 -4.2
Nuclear Periphery 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
Nucleolus 0.5 0.5 2.6 3.7 – 0 0 0 0 6.7 5.2 6.3 1.7 2.2 0
Peroxisomes 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
SpindlePole -3.0 -2.1 -2.7 -2.3 – 0 0 0 0 -4.9 -5.3 -6.0 -0.8 -1.1 -0.3
Vacuole 0 0 0 0 – 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 0.8757 0.8593 0.785 0.6256 0.8265 1.001 1.7722 1.6226 1.2486 0.9921 1.1768 1.2084 1.2066 1.1659 0.8012 1.4816 0.4946 0.5356
Actin 0.0125 0 0.0614 0 0.0123 0.0152 0.0158 0.004 0.0073 0.0008 0.0008 0.0004 0.0326 0 0 0 0.0009 0.003
Bud 0.0003 0 0.0002 0 0.0003 0.0001 0.0006 0.0001 0.0001 0.0001 0.0008 0.0001 0.0007 0 0 0 0.0001 0.0001
Bud Neck 0.0044 0.0002 0.0038 0 0.0031 0.0021 0.0032 0.0001 0.0004 0.0002 0.0031 0.0012 0.0027 0.0002 0.0001 0.0001 0.0006 0.0015
Bud Periphery 0.0004 0 0.0003 0 0.0008 0.0002 0.0011 0.0001 0.0002 0.0001 0.0017 0.0003 0.0013 0.0001 0 0 0.0007 0.0002
Bud Site 0.0079 0.0001 0.0008 0 0.0016 0.0002 0.003 0.0002 0.0005 0.0002 0.0011 0.0003 0.0034 0.0002 0 0 0.0003 0.0002
Cell Periphery 0.0002 0 0.0001 0 0.0005 0.0001 0.0003 0 0 0 0.0003 0.0001 0.0005 0 0 0 0.0001 0
Cytoplasm 0.0018 0 0.0002 0 0.0061 0.0018 0.0029 0.0003 0.0001 0.0001 0.007 0.0001 0.001 0 0 0.0001 0.0005 0.0002
Cytoplasmic Foci 0.0111 0 0.0037 0 0.0149 0.0004 0.0115 0.0018 0.0009 0.0092 0.0069 0.005 0.0239 0 0 0 0.0004 0.0027
Eisosomes 0.0002 0 0.0005 0 0.0002 0.0002 0.0002 0 0 0 0.0001 0 0.0002 0 0 0 0.0003 0
Endoplasmic Reticulum 0.0014 0 0.0003 0 0.0021 0.0011 0.0024 0.0003 0.0002 0.0001 0.0027 0.0002 0.0008 0 0 0 0.0002 0.0003
Endosome 0.0107 0 0.0016 0 0.0175 0.0028 0.0174 0.0102 0.0005 0.0095 0.0408 0.0061 0.0151 0 0 0 0.0011 0.0048
Golgi 0.0034 0 0.0028 0 0.0049 0.0017 0.0049 0.0029 0.0006 0.0087 0.0017 0.0029 0.0095 0 0 0 0.0004 0.0018
Lipid Particles 0.0134 0 0.0032 0 0.0171 0.0004 0.0071 0.0007 0.0007 0.0041 0.0091 0.002 0.017 0 0 0 0.0074 0.0044
Mitochondria 0.0045 0.0001 0.0032 0 0.0017 0.0028 0.0045 0.001 0.0007 0.0042 0.0097 0.0011 0.0086 0.0001 0.0001 0.0001 0.0141 0.0008
None 0.0028 0 0.0002 0 0.0088 0.0004 0.0033 0.0001 0.0002 0 0.0028 0.0001 0.0018 0 0 0 0.0017 0.0003
Nuclear Periphery 0.0153 0.0004 0.0112 0.0001 0.0129 0.017 0.0109 0.0019 0.0024 0.0001 0.0183 0.0043 0.0065 0.0002 0.0004 0.0012 0.0369 0.0021
Nucleolus 0.0469 0.0614 0.0517 0.0052 0.1696 0.1039 0.0445 0.0493 0.0456 0.0303 0.2461 0.135 0.0628 0.0772 0.0645 0.062 0.1452 0.1296
Nucleus 0.8385 0.9328 0.843 0.9946 0.6256 0.8438 0.8294 0.9243 0.9305 0.9278 0.5674 0.8373 0.7712 0.9208 0.9342 0.9359 0.7706 0.8418
Peroxisomes 0.0065 0 0.005 0 0.0093 0.0002 0.0077 0.0007 0.0061 0.004 0.0016 0.0008 0.0171 0 0 0 0.0011 0.002
Punctate Nuclear 0.0156 0.0048 0.0062 0 0.0876 0.0046 0.0175 0.0011 0.0027 0.0003 0.0598 0.0015 0.0177 0.0011 0.0004 0.0005 0.0145 0.0038
Vacuole 0.0012 0 0.0002 0 0.0023 0.0005 0.0074 0.0006 0.0001 0.0002 0.013 0.0007 0.0039 0.0001 0 0 0.0007 0.0002
Vacuole Periphery 0.0012 0 0.0003 0 0.0007 0.0005 0.0045 0.0004 0.0001 0.0001 0.005 0.0004 0.0014 0 0 0 0.0022 0.0002

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 6.6028 10.4934 6.4888 10.7436 8.5608 6.8436 9.5046 11.1889 8.9555 11.7793
Translational Efficiency 2.1249 1.2981 2.0754 0.9844 1.5841 1.9263 1.6976 1.4035 1.5842 1.2988

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
1789 226 393 2067 128 1327 2160 1514 1917 1553 2553 3581

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 719.49 880.40 1081.07 1062.54 869.26 806.19 982.84 1016.68 729.49 816.99 997.96 1043.15
Standard Deviation 89.93 136.79 122.98 139.69 94.23 125.82 127.41 146.03 97.67 130.13 131.60 144.19
Intensity Change Log 2 — 0.291185 0.587413 0.562471 — -0.108668 0.177169 0.226006 — 0.086217 0.377488 0.388150

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000316 0.001493 0.001792 0.001237 0.001194 0.000548 0.000866 0.001011 0.000374 0.000686 0.001009 0.001142
Bud Neck 0.004980 0.017284 0.020681 0.045194 0.001858 0.007250 0.029693 0.028034 0.004771 0.008710 0.028306 0.037939
Bud Site 0.001061 0.003080 0.002305 0.004096 0.001439 0.000826 0.001711 0.002714 0.001086 0.001154 0.001803 0.003512
Cell Periphery 0.000363 0.000117 0.000051 0.000100 0.000070 0.000147 0.000041 0.000069 0.000343 0.000143 0.000043 0.000087
Cytoplasm 0.016333 0.004540 0.000325 0.004546 0.000957 0.002613 0.000690 0.005247 0.015306 0.002894 0.000634 0.004842
Cytoplasmic Foci 0.001543 0.000538 0.000055 0.003175 0.000994 0.001359 0.000016 0.000608 0.001507 0.001239 0.000022 0.002090
Eisosomes 0.000032 0.000050 0.000070 0.000038 0.000056 0.000035 0.000049 0.000043 0.000033 0.000037 0.000053 0.000040
Endoplasmic Reticulum 0.001605 0.008503 0.003811 0.003061 0.004609 0.002511 0.002169 0.002989 0.001806 0.003383 0.002422 0.003030
Endosome 0.000483 0.000633 0.000173 0.003581 0.000407 0.000729 0.000129 0.001461 0.000478 0.000715 0.000136 0.002685
Golgi 0.000321 0.000292 0.000301 0.002703 0.000575 0.000730 0.000192 0.001365 0.000338 0.000666 0.000209 0.002137
Lipid Particles 0.000562 0.000556 0.000131 0.000861 0.000459 0.001170 0.000031 0.000114 0.000555 0.001081 0.000047 0.000545
Mitochondria 0.001502 0.005647 0.001714 0.006454 0.001142 0.006159 0.001399 0.002878 0.001478 0.006085 0.001447 0.004942
Mitotic Spindle 0.000691 0.011886 0.005880 0.020706 0.003378 0.007787 0.003779 0.011764 0.000871 0.008384 0.004102 0.016925
None 0.019658 0.003506 0.001579 0.002641 0.005292 0.007198 0.001971 0.002815 0.018699 0.006661 0.001910 0.002715
Nuclear Periphery 0.000279 0.000871 0.000198 0.002462 0.000116 0.000342 0.000231 0.000581 0.000268 0.000419 0.000226 0.001667
Nuclear Periphery Foci 0.000448 0.001291 0.000168 0.000943 0.004949 0.000538 0.000109 0.000253 0.000749 0.000647 0.000118 0.000651
Nucleolus 0.080612 0.085849 0.119122 0.025111 0.103444 0.121713 0.100499 0.045489 0.082136 0.116494 0.103365 0.033727
Nucleus 0.867569* 0.850103* 0.837234* 0.866640* 0.865542* 0.835537* 0.855133* 0.890216* 0.867433* 0.837657* 0.852378* 0.876608*
Peroxisomes 0.000484 0.001141 0.002879 0.000521 0.002677 0.001350 0.000667 0.000582 0.000630 0.001319 0.001007 0.000547
Vacuole 0.000777 0.001629 0.001265 0.003858 0.000585 0.000806 0.000367 0.001245 0.000764 0.000926 0.000505 0.002753
Vacuole Periphery 0.000383 0.000992 0.000266 0.002072 0.000256 0.000652 0.000256 0.000521 0.000374 0.000701 0.000258 0.001416

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 -6.48 -14.31 -7.95 1.29 5.72 3.99 1.21 -0.12 -13.56 -4.68 -4.07 -11.07 -9.86 -8.06 -1.30
Bud Neck -4.91 -12.50 -27.60 -9.77 -11.84 -5.35 -28.88 -23.47 -17.92 0.50 -4.67 -30.13 -34.38 -25.56 -7.05
Bud Site -2.75 -7.40 -9.05 -1.19 -1.86 0.86 -1.20 -2.76 -7.97 -3.68 -0.43 -7.04 -10.35 -10.22 -6.05
Cell Periphery 1.03 1.29 1.16 1.35 -3.25 -0.88 2.21 -0.44 0.81 -6.71 0.88 1.36 1.18 0.79 -7.57
Cytoplasm 4.67 9.12 6.66 0.11 -6.71 -1.89 0.68 -3.58 -1.89 -3.95 7.05 8.92 6.27 -1.93 -6.48
Cytoplasmic Foci 2.71 4.30 1.11 -1.28 -2.68 -0.42 1.36 0.90 2.34 -2.57 0.98 4.54 2.07 0.99 -3.26
Eisosomes -2.17 -4.55 -0.97 2.88 10.35 4.58 1.42 2.38 -6.09 3.27 -0.43 -2.45 -1.09 -3.53 9.84
Endoplasmic Reticulum -6.71 -8.61 -14.84 4.77 1.84 4.10 4.54 2.34 -3.59 -5.29 -6.73 -7.87 -13.24 -0.58 -7.17
Endosome -0.95 2.64 -3.02 -2.42 -3.93 -1.05 1.33 -1.30 -0.51 -2.30 -1.04 3.72 -3.07 -1.89 -4.70
Golgi 0.35 -1.15 -2.37 -2.45 -2.19 -0.46 1.15 -0.55 -0.23 -1.53 -1.69 1.61 -2.53 -1.09 -2.94
Lipid Particles 0.02 1.74 0.66 0.88 -1.32 -1.61 3.88 3.26 2.86 -3.98 -1.20 2.30 1.25 2.41 -2.15
Mitochondria -1.95 -1.78 -5.04 0.44 -4.63 -3.93 -3.64 -5.09 2.56 -3.78 -3.97 -0.77 -5.53 1.88 -6.20
Mitotic Spindle -2.46 -3.40 -9.10 -1.91 -2.62 -1.29 -1.22 -3.64 -3.14 -3.78 -4.39 -6.21 -11.13 -4.85 -6.06
None 9.81 11.97 10.81 -0.23 -7.41 -1.18 3.47 2.16 3.48 -4.11 7.23 11.99 10.96 3.37 -7.12
Nuclear Periphery -2.75 -0.92 -6.11 -3.01 -5.96 -3.47 -4.75 -7.56 -4.63 -5.58 -2.30 -1.15 -7.27 -6.13 -7.09
Nuclear Periphery Foci -1.77 2.10 -0.32 1.67 -2.26 1.14 1.23 1.21 2.36 -0.90 0.46 2.09 1.29 1.75 -2.44
Nucleolus -0.45 -6.59 16.83 7.85 14.09 -1.64 -0.67 5.72 16.85 15.71 -7.34 -7.50 15.46 22.44 24.09*
Nucleus 1.46 5.99 -0.39 -1.67 -6.29 1.94 2.14 -0.70 -5.53 -6.87 4.23 6.41 -1.04 -5.72 -8.74
Peroxisomes -3.29 -9.65 1.10 3.89 10.32 1.41 2.15 2.29 3.41 2.68 -3.22 -4.03 1.62 4.47 10.01
Vacuole -2.00 -2.55 -5.25 -2.63 -2.19 -0.54 0.80 -3.16 -2.68 -3.46 -0.56 0.24 -5.73 -4.78 -6.10
Vacuole Periphery -1.23 0.75 -1.79 0.06 -2.02 -1.48 0.28 -0.96 0.95 -1.28 -1.37 1.58 -1.73 -0.04 -2.47
Standard name
Human Ortholog
Description Defining member of the SET3 histone deacetylase complex; which is a meiosis-specific repressor of sporulation genes; necessary for efficient transcription by RNAPII; one of two yeast proteins that contains both SET and PHD domains; SET3 has a paralog, SET4, that arose from the whole genome duplication
Localization
Cell Percentages nucleus (92%)
Cell Cycle Regulation No
Subcompartmental Group nucleus-4

Set3

Set3


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 (Set3-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