Standard name
Human Ortholog
Description Sphingoid long-chain base kinase; responsible for synthesis of long-chain base phosphates, which function as signaling molecules, regulates synthesis of ceramide from exogenous long-chain bases, localizes to the Golgi and late endosomes; LCB4 has a paralog, LCB5, 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 0.05 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 – 0.12 0 0 0 – 0 0 0 0.05 0.05 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 0.06 0.08 0.05 0 0
Bud Site 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 0.05 0 0 0.06 0.09 0 0 0 0 0 0 0 0 0
Cytoplasm 0.68 0.69 – 0.71 0.73 0.89 0.94 – 0.93 0.95 0.93 0.93 0.7 0.8 0.84 0.41 0.37 0.35 0.16 0.21 0.2 0.25 0.23 0.26
Endoplasmic Reticulum 0.24 0.26 – 0.17 0.18 0.05 0 – 0 0 0 0 0.2 0.14 0.13 0 0 0 0.3 0.21 0.17 0.06 0.09 0.08
Endosome 0 0 – 0.06 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0.05 0 0.06 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
Mitochondria 0 0 – 0 0 0 0 – 0 0 0 0 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 0.08 0.09 0.07 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
Nucleolus 0 0 – 0 0 0 0 – 0 0 0 0 0.05 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
SpindlePole 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 0.07 0.06 – 0 0.08 0 0.05 – 0.05 0 0 0.06 0 0.05 0 0.6 0.58 0.63 0.37 0.46 0.43 0.52 0.57 0.57
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 4 1 – 2 0 2 1 – 2 2 0 4 1 2 1 2 2 2 6 1 0 1 1 0
Bud 1 1 – 6 1 2 4 – 7 4 8 12 1 0 0 0 0 0 1 2 0 0 0 1
Bud Neck 0 0 – 0 0 0 0 – 0 1 0 0 0 1 0 0 0 0 10 9 3 1 2 3
Bud Site 0 0 – 0 0 0 0 – 1 0 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 3 6 – 1 2 4 8 – 1 8 10 7 0 11 20 1 1 1 1 1 0 0 1 0
Cytoplasm 140 102 – 34 105 134 257 – 153 260 203 205 14 138 183 84 81 89 38 36 8 8 28 44
Endoplasmic Reticulum 49 38 – 8 26 7 10 – 1 4 4 1 4 24 29 6 9 6 72 36 6 1 11 14
Endosome 7 0 – 3 0 1 0 – 0 0 0 1 0 2 3 7 6 11 12 5 2 0 1 2
Golgi 0 0 – 0 0 0 0 – 0 0 0 1 0 0 0 0 3 0 0 0 0 0 0 0
Mitochondria 0 0 – 0 0 1 1 – 3 1 5 4 0 0 0 1 0 3 2 0 0 1 0 2
Nucleus 1 2 – 1 2 2 4 – 0 2 2 2 0 0 2 16 19 17 0 0 0 0 0 2
Nuclear Periphery 3 0 – 0 0 0 0 – 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
Nucleolus 0 0 – 1 0 0 0 – 0 1 0 0 1 0 0 0 0 2 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
SpindlePole 1 0 – 0 1 0 2 – 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0
Vac/Vac Membrane 14 9 – 0 11 5 13 – 8 10 7 13 0 8 4 122 129 159 89 81 17 17 70 98
Unique Cell Count 206 147 48 144 151 274 165 274 218 220 20 173 218 205 221 252 240 176 42 34 123 174
Labelled Cell Count 223 159 56 148 158 300 176 293 239 250 21 186 243 240 250 291 240 176 42 34 123 174


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) 7.5 9.1 – 7.4 8.8 7.8 7.3 – 5.9 6.1 5.4 5.9 7.2 8.8 8.3 12.4 12.3 11.6 – 8.1 8.0
Std Deviation (1e-4) 0.9 1.6 – 0.9 1.3 1.5 2.5 – 1.2 1.3 1.0 1.7 1.1 1.4 1.3 2.4 2.3 2.2 – 1.1 1.3
Intensity Change (Log2) – – – – – – – – – – – – – – – – – – – – –


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

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 1.9203 3.128 2.4099 1.5117 1.7659 2.7908 3.1153 4.6203 4.0023 4.2995 3.1869 4.3353 2.2057 3.1902 2.6901 3.1033 2.7078 2.7797
Actin 0.0053 0.0016 0.0091 0.108 0.0014 0.0124 0.0067 0.0012 0.0194 0.001 0.0954 0.0024 0.0792 0.001 0.0232 0.0697 0.0216 0.0057
Bud 0.0005 0.0044 0.0028 0.0008 0.0017 0.0011 0.0007 0.0004 0.0022 0.0025 0.0018 0.0008 0.0009 0.0004 0.0016 0.0028 0.0006 0.0007
Bud Neck 0.0019 0.0039 0.0078 0.0028 0.0037 0.0218 0.0024 0.0023 0.007 0.003 0.0047 0.0143 0.015 0.0019 0.0069 0.0024 0.0023 0.0236
Bud Periphery 0.0016 0.0021 0.0054 0.0021 0.0039 0.0048 0.0014 0.0009 0.0039 0.0057 0.0039 0.0022 0.0012 0.0005 0.0019 0.0074 0.0012 0.0026
Bud Site 0.004 0.0666 0.0198 0.0032 0.0057 0.0014 0.0053 0.0142 0.014 0.0035 0.0119 0.0013 0.0169 0.0283 0.0203 0.0036 0.0012 0.0014
Cell Periphery 0.0771 0.0526 0.0373 0.0306 0.0201 0.0592 0.0471 0.0489 0.0393 0.0264 0.0054 0.0328 0.0211 0.0229 0.0167 0.0119 0.0074 0.0181
Cytoplasm 0.3857 0.4791 0.4935 0.2667 0.3586 0.4943 0.4139 0.477 0.4826 0.3619 0.2902 0.5243 0.3582 0.3972 0.4518 0.2238 0.3551 0.5031
Cytoplasmic Foci 0.0402 0.0245 0.0239 0.0648 0.0186 0.0311 0.0339 0.0286 0.0355 0.0261 0.0391 0.0213 0.0591 0.0394 0.0274 0.0402 0.0463 0.0303
Eisosomes 0.0003 0.0007 0.0002 0.0007 0.0001 0.0004 0.0002 0.0002 0.0003 0 0.0007 0 0.0004 0 0.0002 0.0003 0.0001 0
Endoplasmic Reticulum 0.023 0.0196 0.0221 0.0152 0.0095 0.0239 0.0246 0.0284 0.0147 0.0124 0.0117 0.021 0.0225 0.0336 0.033 0.013 0.0065 0.0276
Endosome 0.1397 0.1091 0.082 0.1175 0.0931 0.0829 0.0842 0.0688 0.0667 0.1317 0.1406 0.0771 0.1083 0.1046 0.1148 0.1731 0.2748 0.1014
Golgi 0.0115 0.0057 0.0081 0.0138 0.0241 0.0078 0.0083 0.0031 0.0063 0.0201 0.0311 0.0081 0.0233 0.0039 0.0115 0.0087 0.0229 0.009
Lipid Particles 0.0427 0.0242 0.037 0.0773 0.0439 0.0173 0.0476 0.0668 0.0317 0.0198 0.0374 0.0206 0.0493 0.0544 0.0326 0.0082 0.0224 0.0215
Mitochondria 0.0067 0.0014 0.0101 0.0037 0.0024 0.0076 0.0049 0.0002 0.005 0.0116 0.0366 0.0016 0.0031 0.0002 0.0014 0.0144 0.0018 0.0013
None 0.0149 0.0469 0.0166 0.0119 0.0072 0.0156 0.036 0.0345 0.0159 0.0107 0.0119 0.0147 0.0186 0.0196 0.0364 0.0026 0.0023 0.0113
Nuclear Periphery 0.0069 0.0024 0.0018 0.0057 0.0016 0.0015 0.0039 0.0023 0.0013 0.0028 0.0077 0.0031 0.0032 0.0022 0.0028 0.0026 0.0024 0.002
Nucleolus 0.0014 0.0011 0.0007 0.0007 0.0006 0.0003 0.0006 0.0007 0.0006 0.0034 0.0042 0.0004 0.0009 0.0007 0.0006 0.0004 0.0003 0.0005
Nucleus 0.002 0.0033 0.0017 0.0038 0.0017 0.0012 0.0018 0.0021 0.0019 0.0029 0.0087 0.0026 0.0018 0.0019 0.0021 0.0018 0.0009 0.0019
Peroxisomes 0.0067 0.0003 0.0085 0.0378 0.0041 0.003 0.015 0.0003 0.0101 0.0051 0.0152 0.0003 0.009 0.0003 0.0013 0.0034 0.0395 0.0009
Punctate Nuclear 0.0013 0.0025 0.0005 0.0129 0.0006 0.0004 0.0068 0.001 0.0011 0.0021 0.0382 0.0004 0.0027 0.0008 0.0017 0.0013 0.005 0.0007
Vacuole 0.2217 0.1459 0.2069 0.2153 0.3876 0.207 0.2502 0.216 0.2368 0.3356 0.1975 0.2455 0.2026 0.2826 0.2063 0.3954 0.1769 0.2316
Vacuole Periphery 0.0049 0.0023 0.0044 0.0044 0.01 0.0051 0.0045 0.0023 0.0038 0.0116 0.0062 0.0052 0.0027 0.0036 0.0056 0.0129 0.0082 0.0048

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 29.1299 32.6162 32.0099 32.1449 24.0343 28.8197 33.5101 29.2586 35.8862 30.5358
Translational Efficiency 1.2855 1.3799 1.1289 1.1307 1.1517 1.3178 1.1813 1.2582 0.9872 1.1191

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Sphingoid long-chain base kinase; responsible for synthesis of long-chain base phosphates, which function as signaling molecules, regulates synthesis of ceramide from exogenous long-chain bases, localizes to the Golgi and late endosomes; LCB4 has a paralog, LCB5, that arose from the whole genome duplication
Localization
Cell Percentages ER (19%), cytoplasm (11%), mixed (52%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Lcb4

Lcb4


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 (Lcb4-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