Standard name
Human Ortholog
Description Sorting nexin; involved in retrieval of late-Golgi SNAREs from post-Golgi endosomes to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX phosphoinositide-binding domain; forms complexes with Snx41p and with Atg20p
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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 0.07 0 0 0 0 0.05 0 0 0 0 0 0
Bud 0 0 0 0 0.05 0.08 0.09 0.1 0.09 0.09 0.12 0.12 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 0.14 0.18 0.08 0.12 0.12 0.12 0.13 0.13 0.09 0.18 0.16 0.15 0.13 0.14 0.14 0.13 0.16 0.11 0.05 0 0 0.05 0.05 0.05
Endoplasmic Reticulum 0 0.08 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0
Endosome 0.6 0.43 0.82 0.63 0.66 0.55 0.43 0.53 0.42 0.27 0.22 0.27 0.68 0.72 0.7 0.61 0.58 0.7 0.7 0.79 0.8 0.67 0.76 0.72
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 0.21 0.12 0 0.16 0.1 0.21 0.28 0.2 0.31 0.41 0.53 0.36 0 0 0 0.05 0.06 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 0.05 0 0 0.07 0 0.06 0.07 0.06 0.06 0 0 0 0.09 0.07 0.06 0 0 0 0 0 0
Peroxisomes 0 0 0.07 0.23 0.15 0.16 0.09 0.13 0.08 0 0 0.07 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0.13 0 0.25 0.28 0.26 0.24 0.25 0.29 0.23 0.15 0.13 0.24 0.26 0.28 0.25 0.28 0.26 0.28 0.08 0 0.07 0.1 0.07 0.06
Vac/Vac Membrane 0.13 0.24 0.08 0 0.05 0 0 0 0 0.05 0.05 0 0.12 0.18 0.18 0.16 0.17 0.12 0 0.06 0 0.07 0 0.07
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 3 2 1 2 3 1 10 4 4 6 1 8 18 4 14 7 6 8 5 2 2 1 1 2
Bud 8 5 5 6 12 22 28 32 28 30 38 41 8 3 4 4 3 2 1 3 1 2 1 2
Bud Neck 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 2 1 1 3 0 4
Bud Site 1 0 0 1 0 1 3 1 2 2 3 5 0 0 0 0 0 1 – – – – – –
Cell Periphery 0 0 0 1 0 0 0 1 1 5 4 6 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 46 27 16 19 31 33 42 42 28 57 49 55 32 67 66 30 26 17 19 5 2 16 20 19
Endoplasmic Reticulum 4 12 4 1 2 7 5 2 3 8 2 4 6 0 6 3 9 6 5 1 2 2 2 1
Endosome 193 65 173 103 171 155 139 173 124 85 68 97 166 349 335 137 93 103 252 143 181 218 313 297
Golgi 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 8 4 2 7 1 4 1 3 3
Mitochondria 69 18 3 26 26 60 93 65 93 130 164 127 2 1 0 11 9 3 15 2 4 11 15 11
Nucleus 1 0 1 0 1 0 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 1 1 1
Nuclear Periphery 1 1 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 1 1 2 1 3
Nucleolus 8 6 5 8 10 11 23 12 18 22 19 22 11 15 12 20 12 9 0 0 0 2 2 2
Peroxisomes 10 0 15 37 40 46 31 44 23 14 9 26 0 7 12 1 1 2 3 0 2 0 0 0
SpindlePole 41 6 53 46 68 69 83 95 69 48 39 86 63 136 119 62 41 41 29 4 16 31 27 25
Vac/Vac Membrane 41 37 16 2 14 8 6 6 10 15 14 12 29 85 87 35 27 18 12 11 2 23 16 28
Unique Cell Count 321 152 211 164 259 282 327 327 296 318 308 356 245 484 482 225 160 148 362 182 226 325 411 412
Labelled Cell Count 427 180 292 252 378 413 463 479 405 423 410 490 336 669 656 318 231 212 362 182 226 325 411 412


Endosome

(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) 5.8 6.8 7.0 6.2 7.0 6.3 6.1 6.3 6.0 5.7 5.4 5.7 7.9 8.7 8.5 10.7 9.9 10.4 7.8 8.0 8.6
Std Deviation (1e-4) 0.7 1.2 1.2 1.1 1.7 1.0 1.1 1.4 1.4 1.5 1.3 1.2 1.1 1.0 1.0 1.9 1.8 1.8 1.0 1.1 1.3
Intensity Change (Log2) – – – -0.17 0.0 -0.15 -0.19 -0.15 -0.2 -0.28 -0.35 -0.29 0.19 0.32 0.29 0.62 0.51 0.58 0.16 0.2 0.31


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 3.7 0 0 0 0 0
Bud 0 1.3 2.6 2.9 3.3 3.2 3.2 4.0 3.9 0.6 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 0 0 0 0 0 0 0 0 0 0
Cytoplasm 1.3 1.6 1.5 1.9 1.9 0.7 3.4 2.8 2.7 1.9 2.3 2.3 2.0 2.6 1.3
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 1.9 0
Endosome -4.2 -3.9 -6.3 -9.1 -6.9 -9.0 -12.5 -13.4 -12.6 -3.5 -2.8 -3.4 -4.9 -5.1 -2.7
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 5.2 3.9 6.5 8.0 6.3 8.5 10.2 12.4 9.4 0 0 0 2.1 2.3 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 1.3 0.9 0.9 2.4 0.8 2.0 2.3 2.0 2.1 1.2 0.5 0.1 2.9 2.3 1.8
Peroxisomes 4.3 2.8 3.1 1.0 2.3 0.3 -1.3 -2.2 0.1 -4.2 -3.9 -2.9 -3.7 -3.0 -2.5
SpindlePole 0.6 0.3 -0.2 0.1 1.0 -0.5 -2.9 -3.6 -0.3 0.1 0.8 -0.1 0.6 0.1 0.5
Vacuole -2.9 -1.0 -2.4 -3.3 -3.3 -2.1 -1.4 -1.5 -2.2 1.5 3.4 3.6 2.6 2.8 1.5

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 3.4897 4.3357 3.9584 3.9469 3.2825 3.9012 2.2926 3.0848 2.9551 2.9156 2.8308 2.8071 1.8574 3.1323 2.7029 2.8405 2.0192 2.5798
Actin 0.0118 0.0002 0.0094 0.0349 0.0004 0.001 0.0175 0.0002 0.0017 0.0029 0 0.0032 0.0144 0.0011 0.0028 0.0003 0.0003 0.0054
Bud 0.0013 0.0001 0.0006 0.001 0.0001 0.0002 0.0005 0.001 0.0004 0.0002 0 0.0027 0.0024 0.0225 0.0171 0.0045 0.0001 0.0031
Bud Neck 0.0008 0.0002 0.0008 0.0012 0.0003 0.001 0.0035 0.0003 0.001 0.0002 0.0001 0.0007 0.0008 0.0003 0.0012 0.0002 0.0001 0.0012
Bud Periphery 0.0005 0 0.0004 0.0007 0.0001 0.0001 0.0005 0.0002 0.0004 0.0001 0 0.0008 0.0015 0.0063 0.0042 0.0023 0.0001 0.0016
Bud Site 0.0035 0.0009 0.0035 0.001 0.0005 0.0003 0.0053 0.0026 0.0069 0.0006 0 0.0005 0.003 0.0113 0.0082 0.0004 0.0002 0.0005
Cell Periphery 0.0003 0.0002 0.0002 0.0001 0 0.0001 0.0005 0.0001 0.0001 0 0 0.0001 0.0002 0.0004 0.0005 0.0001 0 0.0001
Cytoplasm 0.1681 0.2625 0.1383 0.1625 0.0957 0.1506 0.1157 0.192 0.1288 0.085 0.0278 0.1729 0.1297 0.237 0.088 0.1083 0.0627 0.1499
Cytoplasmic Foci 0.2154 0.1804 0.2411 0.2146 0.3086 0.2905 0.173 0.296 0.2687 0.1812 0.2849 0.2466 0.23 0.3069 0.3026 0.2171 0.3278 0.2954
Eisosomes 0.0001 0 0.0004 0.0001 0 0 0.0001 0 0 0 0 0 0.0002 0 0 0 0 0.0001
Endoplasmic Reticulum 0.0076 0.006 0.0052 0.0016 0.002 0.0042 0.0057 0.0029 0.0028 0.0014 0.0057 0.007 0.0047 0.0022 0.006 0.0011 0.0054 0.0045
Endosome 0.4812 0.4313 0.4868 0.5041 0.4806 0.4516 0.5271 0.4507 0.5215 0.6593 0.6376 0.5045 0.4433 0.3606 0.4825 0.6112 0.5242 0.4502
Golgi 0.0152 0.0126 0.0205 0.0165 0.0204 0.0251 0.0398 0.012 0.0198 0.0205 0.0118 0.0206 0.0175 0.0108 0.0163 0.0133 0.023 0.02
Lipid Particles 0.0289 0.0288 0.0136 0.0022 0.0154 0.027 0.0305 0.0114 0.009 0.0055 0.0021 0.0048 0.0487 0.0095 0.0075 0.0039 0.0201 0.0144
Mitochondria 0.0031 0.0003 0.0018 0.0008 0.0005 0.0025 0.0096 0.0007 0.0053 0.0007 0.0003 0.0018 0.0048 0.0016 0.0037 0.0009 0.0022 0.0068
None 0.0327 0.0397 0.0438 0.0147 0.045 0.0194 0.005 0.0044 0.0013 0.0011 0.0003 0.0022 0.0305 0.0053 0.0149 0.0142 0.007 0.0088
Nuclear Periphery 0.0015 0.0022 0.0027 0.0007 0.0006 0.0007 0.0041 0.0014 0.0011 0.0018 0.001 0.0063 0.0075 0.0011 0.0036 0.001 0.0038 0.0066
Nucleolus 0.0016 0.0002 0.0004 0.0003 0.0001 0.0003 0.0008 0.0002 0.0003 0.0002 0 0.0003 0.0007 0.0006 0.0021 0.0003 0.0001 0.0005
Nucleus 0.0021 0.0009 0.0044 0.0007 0.0003 0.0005 0.0107 0.0008 0.0012 0.0009 0.0001 0.0014 0.0116 0.0013 0.0052 0.0011 0.0005 0.0014
Peroxisomes 0.0044 0.0091 0.0039 0.0045 0.0144 0.0109 0.0124 0.0029 0.0107 0.0058 0.0087 0.004 0.0269 0.0071 0.0108 0.0025 0.0096 0.0131
Punctate Nuclear 0.0018 0.0008 0.0028 0.0013 0.0018 0.001 0.0084 0.003 0.0027 0.0132 0.0004 0.0036 0.0096 0.0024 0.0039 0.0015 0.0026 0.0044
Vacuole 0.0162 0.0214 0.0162 0.0331 0.0112 0.0111 0.0245 0.015 0.0133 0.0143 0.0142 0.0124 0.01 0.0101 0.0152 0.0119 0.0077 0.0091
Vacuole Periphery 0.002 0.0021 0.0031 0.0037 0.0019 0.002 0.0047 0.0022 0.0028 0.0047 0.0049 0.0038 0.0023 0.0019 0.0037 0.0038 0.0026 0.003

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 13.0118 10.0809 10.3576 15.236 12.934 13.0046 17.0533 18.7862 19.7506 16.8793
Translational Efficiency 1.6406 1.9882 1.9372 1.5428 1.3722 2.504 1.5042 1.3786 1.3473 1.2623

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✔
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Sorting nexin; involved in retrieval of late-Golgi SNAREs from post-Golgi endosomes to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX phosphoinositide-binding domain; forms complexes with Snx41p and with Atg20p
Localization
Cell Percentages endosome (66%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Snx4

Snx4


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 (Snx4-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