Standard name
Human Ortholog
Description Histone deacetylase, component of both the Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the arginine methyltransferase, Hmt1p
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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
Bud 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
Bud Site 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
Cytoplasm 0 0 0 0.05 0.07 0 0 0 0 0 0 0 0.07 0.12 0.17 – – – 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
Endosome 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
Mitochondria 0.22 0 0 0.06 0 0.16 0.19 0.08 0.09 0.17 0.19 0.13 0 0 0 – – – 0 0 0 0 0 0
Nucleus 0.83 0.86 0.89 0.87 0.81 0.77 0.73 0.67 0.71 0.66 0.65 0.65 0.9 0.84 0.78 – – – 0.63 0.7 0.58 0.75 0.68 0.59
Nuclear Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 – – – 0 0 0 0 0 0
Nucleolus 0.28 0.19 0.12 0.17 0.18 0.27 0.34 0.38 0.42 0.44 0.5 0.51 0.05 0 0.05 – – – 0.25 0.22 0.3 0.13 0.16 0.22
Peroxisomes 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
Vac/Vac Membrane 0 0.06 0 0 0 0 0 0 0 0 0 0 0 0 0 – – – 0 0 0 0 0.06 0.06
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 1 0 0 0 0
Bud 0 0 0 0 2 3 12 7 2 3 2 3 0 0 0 – – – 1 4 6 3 4 4
Bud Neck 0 0 0 0 1 1 4 5 0 0 4 3 0 0 0 – – – 0 0 2 1 0 2
Bud Site 0 0 1 0 2 11 22 16 13 21 24 19 0 0 0 – – – – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 – – – 0 0 0 0 0 0
Cytoplasm 1 4 10 13 25 15 15 23 9 4 4 7 37 66 83 – – – 0 1 2 5 4 7
Endoplasmic Reticulum 0 1 1 0 1 0 0 0 0 0 0 0 0 0 1 – – – 0 0 0 0 1 2
Endosome 0 2 13 1 3 2 2 2 0 0 0 0 1 1 3 – – – 3 1 11 5 8 13
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 – – – 3 2 1 0 1 2
Mitochondria 40 7 6 15 13 94 122 56 43 98 118 90 1 0 1 – – – 1 0 1 1 5 5
Nucleus 152 218 443 230 281 463 472 442 340 380 411 440 447 445 376 – – – 119 199 317 319 302 290
Nuclear Periphery 0 0 4 2 2 5 10 11 7 6 8 8 0 2 0 – – – 0 0 4 1 3 2
Nucleolus 52 48 61 44 61 166 221 250 202 252 315 345 27 19 24 – – – 48 61 166 53 69 109
Peroxisomes 0 0 0 1 0 0 0 0 0 0 0 0 0 0 5 – – – 0 0 1 0 0 0
SpindlePole 0 1 4 0 0 1 2 0 0 2 1 1 6 13 10 – – – 2 1 13 10 8 20
Vac/Vac Membrane 3 14 3 1 5 9 6 4 3 5 2 3 1 4 4 – – – 6 8 17 16 25 28
Unique Cell Count 183 254 497 263 348 605 649 663 482 578 631 672 496 528 481 191 284 549 428 444 497
Labelled Cell Count 248 295 546 307 396 770 888 816 619 771 889 919 520 551 507 191 284 549 428 444 497


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) 6.4 8.8 7.8 7.2 7.6 6.8 6.8 6.9 7.2 7.2 6.6 6.8 9.4 9.2 8.6 – – – 8.8 8.9 9.4
Std Deviation (1e-4) 1.3 1.3 1.7 2.2 2.2 2.1 1.8 2.0 2.1 2.1 2.2 1.8 1.6 1.7 1.7 – – – 1.4 1.4 1.8
Intensity Change (Log2) – – – -0.11 -0.04 -0.19 -0.2 -0.16 -0.11 -0.11 -0.23 -0.18 0.28 0.25 0.15 – – – 0.18 0.2 0.27


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 – – –
Bud 0 0 0 3.0 0 0 0 0 0 0 0 0 – – –
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 – – –
Bud Site 0 0 2.6 3.8 3.1 3.3 4.0 4.1 3.4 0 0 0 – – –
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 – – –
Cytoplasm 2.2 3.7 0.5 0.3 1.5 -0.2 -1.9 -2.1 -1.4 4.0 6.4 8.1 – – –
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 – – –
Endosome 0 -1.8 -3.3 -3.4 -3.5 -3.6 -3.9 -4.1 -4.2 -3.2 -3.3 -2.5 – – –
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 – – –
Mitochondria 3.6 2.4 8.2 9.4 5.4 5.5 8.7 9.3 7.5 0 0 0 – – –
Nucleus -0.7 -3.4 -5.4 -6.9 -8.9 -7.3 -9.0 -9.3 -9.3 0.5 -2.3 -4.6 – – –
Nuclear Periphery 0 0 0 1.1 1.3 1.0 0 0.8 0.6 0 0 0 – – –
Nucleolus 1.7 2.1 6.2 8.5 9.7 10.5 11.3 13.3 13.9 -3.8 -5.2 -4.0 – – –
Peroxisomes 0 0 0 0 0 0 0 0 0 0 0 0 – – –
SpindlePole 0 0 0 0 0 0 0 0 0 0 2.1 1.7 – – –
Vacuole 0 0 1.4 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 7.3829 7.3276 6.8896 6.2458 6.5355 6.3343 5.6469 5.6369 5.4087 4.8523 4.5993 5.4717 5.8471 5.3352 4.9264 5.3245 4.4619 4.7559
Actin 0.0003 0 0.0001 0 0.0001 0 0.0265 0 0.0049 0 0.102 0.0008 0.0032 0 0.0055 0 0.0413 0
Bud 0.0001 0 0 0 0.0001 0 0.0013 0 0.0003 0 0.0077 0.0004 0.0005 0 0.0002 0 0.0002 0.0001
Bud Neck 0.0005 0.0001 0.0001 0 0.0003 0.0007 0.0018 0.0002 0.0004 0 0.001 0.0014 0.0003 0.0001 0.0002 0 0.0007 0.0008
Bud Periphery 0.0002 0 0.0001 0 0.0003 0.0001 0.0017 0 0.0007 0 0.0139 0.0009 0.0006 0 0.0002 0 0.0005 0.0001
Bud Site 0.0003 0.0001 0.0001 0 0.0003 0.0001 0.0123 0.0001 0.0121 0 0.007 0.0007 0.0022 0 0.0012 0 0.0005 0.0001
Cell Periphery 0 0 0 0 0.0001 0 0.0004 0 0.0008 0 0.0002 0.0002 0 0 0.0001 0 0.0001 0
Cytoplasm 0.001 0.0001 0.0004 0 0 0 0.0041 0.0001 0.0004 0 0.0004 0.0005 0.0057 0 0.0087 0 0.0001 0
Cytoplasmic Foci 0.0001 0 0.0002 0 0 0 0.05 0 0.0035 0 0.0065 0.0027 0.016 0 0.0047 0 0.0003 0
Eisosomes 0 0 0 0 0 0 0.0003 0 0 0 0.0002 0 0 0 0 0 0.0005 0
Endoplasmic Reticulum 0.0005 0 0.0002 0 0 0 0.0017 0 0 0 0.0004 0.0005 0.002 0 0.0062 0 0.0032 0
Endosome 0.0006 0 0.002 0 0.0001 0 0.02 0 0.0002 0 0.0094 0.0067 0.018 0 0.0067 0 0.005 0
Golgi 0 0 0.0005 0 0 0 0.0112 0 0.0005 0 0.0211 0.0014 0.005 0 0.0042 0 0.0073 0
Lipid Particles 0 0 0.0056 0 0.0001 0 0.0202 0 0.0003 0 0.0054 0.0008 0.005 0 0.0016 0 0.0016 0
Mitochondria 0.0007 0.0001 0.0019 0 0.0011 0.0001 0.0105 0.0001 0.0003 0.0001 0.0184 0.012 0.0019 0.0001 0.0098 0.0001 0.0109 0.0001
None 0.0002 0 0.0014 0 0.0001 0 0.003 0 0.0001 0 0.0003 0.0001 0.0024 0 0.0023 0 0.0004 0
Nuclear Periphery 0.0072 0.0036 0.0048 0.0001 0.0012 0.0001 0.0017 0.0002 0.0004 0.0002 0.0009 0.0011 0.0058 0.0003 0.01 0.0003 0.0052 0.0002
Nucleolus 0.055 0.0375 0.0335 0.0142 0.2228 0.111 0.0552 0.0288 0.0318 0.0185 0.1235 0.1263 0.0275 0.0318 0.0282 0.0311 0.2586 0.1129
Nucleus 0.927 0.9499 0.9466 0.9854 0.7694 0.8809 0.7392 0.9696 0.9367 0.9811 0.672 0.8288 0.8722 0.967 0.902 0.9684 0.6606 0.8848
Peroxisomes 0 0 0.0002 0 0.0001 0 0.0251 0 0.0032 0 0.0058 0.0118 0.0055 0 0.0011 0 0.0003 0
Punctate Nuclear 0.0052 0.0083 0.0009 0.0002 0.0035 0.0069 0.0105 0.0008 0.0031 0.0001 0.0024 0.0007 0.0253 0.0005 0.0062 0.0001 0.0015 0.0007
Vacuole 0.0007 0.0001 0.0007 0 0.0002 0.0001 0.0025 0 0.0004 0 0.0008 0.0015 0.0005 0 0.0007 0 0.0004 0.0001
Vacuole Periphery 0.0003 0 0.0009 0 0.0002 0 0.0007 0 0.0001 0 0.0006 0.0008 0.0004 0 0.0005 0 0.0008 0

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 29.6614 34.8489 30.3567 38.6779 39.0067 39.809 31.4057 40.3255 43.4485 41.5864
Translational Efficiency 1.3518 0.9308 0.9222 0.837 0.8836 0.8526 1.2301 0.7592 0.8084 0.9549

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
966 846 611 1184 2174 157 1866 1334 3140 1003 2477 2518

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 859.89 970.53 1253.57 1283.32 885.44 1030.77 1216.56 1307.78 877.58 979.96 1225.69 1296.28
Standard Deviation 119.20 158.78 175.41 245.31 125.49 132.38 178.23 239.06 124.15 156.49 178.25 242.33
Intensity Change Log 2 — 0.174621 0.543819 0.577657 — 0.219256 0.458341 0.562653 — 0.197438 0.501087 0.570065

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000675 0.001410 0.001340 0.002487 0.000477 0.001971 0.001244 0.001558 0.000538 0.001498 0.001268 0.001995
Bud Neck 0.005807 0.013923 0.022989 0.046212 0.011021 0.009313 0.032746 0.033968 0.009417 0.013202 0.030339 0.039726
Bud Site 0.000594 0.001668 0.002422 0.024407 0.001583 0.002395 0.003391 0.034418 0.001279 0.001782 0.003152 0.029711
Cell Periphery 0.000045 0.000063 0.000068 0.000326 0.000061 0.000094 0.000087 0.000288 0.000056 0.000068 0.000082 0.000306
Cytoplasm 0.000995 0.001938 0.001048 0.007685 0.000620 0.002326 0.001826 0.008946 0.000736 0.001999 0.001634 0.008353
Cytoplasmic Foci 0.000164 0.000824 0.000205 0.034959 0.000186 0.002519 0.000663 0.058479 0.000179 0.001089 0.000550 0.047419
Eisosomes 0.000034 0.000045 0.000075 0.000076 0.000030 0.000057 0.000058 0.000072 0.000031 0.000047 0.000062 0.000074
Endoplasmic Reticulum 0.003217 0.004319 0.001713 0.003070 0.002574 0.005966 0.002312 0.001615 0.002772 0.004577 0.002164 0.002299
Endosome 0.000203 0.000691 0.000105 0.007581 0.000232 0.001223 0.000816 0.010601 0.000223 0.000775 0.000640 0.009181
Golgi 0.000220 0.000652 0.000261 0.008468 0.000170 0.002324 0.000576 0.013137 0.000185 0.000914 0.000499 0.010941
Lipid Particles 0.000327 0.001185 0.000072 0.001051 0.000262 0.006416 0.000101 0.002990 0.000282 0.002004 0.000094 0.002078
Mitochondria 0.002895 0.003521 0.002055 0.008211 0.001256 0.002936 0.002826 0.009610 0.001760 0.003429 0.002636 0.008952
Mitotic Spindle 0.002473 0.004767 0.003541 0.331874* 0.002010 0.031525 0.027971 0.572585* 0.002153 0.008955 0.021945 0.459399*
None 0.002549 0.003056 0.001558 0.003537 0.001534 0.002193 0.003878 0.003461 0.001846 0.002921 0.003306 0.003497
Nuclear Periphery 0.000215 0.000242 0.000138 0.002791 0.000552 0.000248 0.000480 0.001916 0.000448 0.000243 0.000396 0.002327
Nuclear Periphery Foci 0.000677 0.001355 0.000310 0.005109 0.000488 0.001335 0.000872 0.006515 0.000546 0.001352 0.000733 0.005854
Nucleolus 0.108703 0.125209 0.118085 0.111100 0.102310 0.084603 0.105686 0.071431 0.104277 0.118853 0.108744 0.090084
Nucleus 0.868885* 0.832524* 0.840120* 0.363769* 0.873528* 0.834677* 0.810802* 0.125490 0.872100* 0.832861* 0.818034* 0.237532*
Peroxisomes 0.000915 0.001738 0.002955 0.022769 0.000698 0.005925 0.001616 0.028173 0.000765 0.002394 0.001947 0.025632
Vacuole 0.000235 0.000533 0.000690 0.010580 0.000223 0.001622 0.001521 0.011863 0.000227 0.000703 0.001316 0.011259
Vacuole Periphery 0.000173 0.000335 0.000248 0.003940 0.000184 0.000331 0.000530 0.002882 0.000180 0.000334 0.000461 0.003380

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 -5.11 -10.03 -7.78 -3.27 -3.82 -4.79 -16.85 -6.21 0.76 -1.42 -7.30 -19.39 -9.96 -2.37 -3.51
Bud Neck -8.15 -14.99 -18.62 -14.43 -10.19 0.99 -21.38 -16.68 -15.35 -4.69 -4.52 -25.51 -24.31 -19.92 -8.99
Bud Site -3.00 -7.73 -16.09 -15.00 -14.54 -1.37 -7.01 -17.86 -16.28 -16.19 -1.40 -8.85 -23.49 -22.82 -21.12
Cell Periphery -2.79 -1.83 -13.88 -12.50 -10.72 -1.45 -2.94 -11.97 -6.58 -12.18 -1.41 -3.69 -16.74 -17.03 -16.36
Cytoplasm -1.17 -0.07 -4.13 -2.84 -3.55 -1.25 -3.65 -9.31 -2.80 -7.49 -2.05 -2.33 -9.54 -4.87 -7.77
Cytoplasmic Foci -1.63 -0.06 -11.70 -11.37 -11.69 -1.80 -3.17 -14.71 -13.16 -14.36 -2.27 -3.19 -18.75 -18.10 -18.32
Eisosomes -4.70 -13.59 -14.32 -8.72 -0.36 -5.73 -19.11 -15.33 -2.47 -4.39 -7.70 -23.35 -21.25 -9.67 -4.79
Endoplasmic Reticulum -3.73 6.40 1.84 5.05 -3.55 -5.46 -0.06 1.85 5.85 1.80 -7.39 3.13 2.15 7.95 -0.09
Endosome -1.82 2.26 -5.06 -3.88 -5.24 -2.16 -2.14 -7.38 -4.66 -6.47 -2.34 -1.96 -8.88 -6.69 -7.86
Golgi -1.73 -0.57 -3.38 -2.94 -3.34 -1.53 -4.84 -4.94 -2.11 -4.50 -2.49 -4.72 -5.98 -4.81 -5.48
Lipid Particles -1.23 1.72 -3.15 0.43 -9.19 -1.59 1.08 -5.41 1.17 -6.70 -2.03 1.72 -6.29 0.72 -9.13
Mitochondria -0.32 0.43 -2.23 -1.79 -7.40 -1.24 -5.32 -5.74 -2.35 -3.94 -1.31 -2.05 -6.63 -2.26 -6.45
Mitotic Spindle -0.94 -1.00 -26.35* -25.92* -25.95* -2.52 -12.44 -43.10* -27.69* -35.94* -2.70 -12.27 -48.47 -45.50* -40.37*
None -1.12 2.50 -3.61 -2.36 -7.75 -0.95 -6.08 -6.45 -1.70 -0.45 -3.35 -4.63 -8.24 -2.71 -2.41
Nuclear Periphery -0.97 0.72 -11.93 -11.74 -12.28 1.67 -1.14 -9.17 -13.39 -10.93 1.87 -1.35 -13.28 -18.01 -15.07
Nuclear Periphery Foci -1.92 2.51 -7.69 -5.64 -8.48 -1.59 -2.76 -7.64 -6.01 -4.74 -2.39 -2.47 -10.72 -7.73 -6.96
Nucleolus -2.90 -3.05 -8.89 -6.15 -5.02 1.90 -7.28 -3.98 -4.07 2.23 -3.32 -7.83 -9.57 -4.92 -1.86
Nucleus 5.28 5.74 43.80* 38.67 36.50 2.23 18.56 78.93* 32.47 52.60* 6.76 19.24 82.77* 63.16* 56.79
Peroxisomes -2.36 -6.44 -14.09 -13.43 -12.23 -1.63 -6.30 -17.14 -5.46 -15.90 -2.88 -8.49 -22.15 -18.24 -20.22
Vacuole -3.69 -5.06 -8.69 -8.32 -8.14 -2.77 -4.33 -9.80 -6.52 -7.44 -4.41 -4.75 -13.10 -12.07 -10.18
Vacuole Periphery -3.08 -4.79 -3.83 -3.40 -3.59 -2.07 -2.85 -6.56 -5.40 -5.07 -3.38 -3.27 -6.48 -5.64 -5.42
Standard name
Human Ortholog
Description Histone deacetylase, component of both the Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the arginine methyltransferase, Hmt1p
Localization
Cell Percentages nucleus (99%)
Cell Cycle Regulation No
Subcompartmental Group nucleus-4

Rpd3

Rpd3


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 (Rpd3-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