YDR062W / LCB2

Component of serine palmitoyltransferase, responsible along with Lcb1p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine

Zygosity: Heterozygous strain
fixedexpanded
Profile for YDR062W / LCB2

Click on Significant Values for Screen Details ID:SGTC_35|Compound:0133-0054|FD-Score:3.90|P-value:9.14E-5 ID:SGTC_37|Compound:0566-0070|FD-Score:3.52|P-value:3.71E-4 ID:SGTC_115|Compound:0527-0192|FD-Score:3.81|P-value:1.32E-4 ID:SGTC_360|Compound:0957-0399|FD-Score:-3.39|P-value:6.15E-4 ID:SGTC_365|Compound:0121-0052|FD-Score:3.96|P-value:7.24E-5 ID:SGTC_369|Compound:0957-0393|FD-Score:3.89|P-value:9.51E-5 ID:SGTC_372|Compound:0155-0182|FD-Score:7.72|P-value:7.25E-14 ID:SGTC_376|Compound:3970-0862|FD-Score:4.23|P-value:2.53E-5 ID:SGTC_457|Compound:grayanotoxin iii|FD-Score:5.22|P-value:2.78E-7 ID:SGTC_528|Compound:3492-0019|FD-Score:5.16|P-value:3.87E-7 ID:SGTC_597|Compound:k018-0003|FD-Score:3.24|P-value:9.36E-4 ID:SGTC_628|Compound:1636-0253|FD-Score:3.65|P-value:2.32E-4 ID:SGTC_671|Compound:0560-0003|FD-Score:5.79|P-value:1.48E-8 ID:SGTC_802|Compound:4112-3352|FD-Score:3.53|P-value:3.55E-4 ID:SGTC_812|Compound:4251-0442|FD-Score:3.92|P-value:8.64E-5 ID:SGTC_866|Compound:0495-0101|FD-Score:4.19|P-value:2.97E-5 ID:SGTC_1215|Compound:3852-0577|FD-Score:-3.69|P-value:2.17E-4 ID:SGTC_1219|Compound:1469-0211|FD-Score:3.67|P-value:2.14E-4 ID:SGTC_1228|Compound:0124-0032|FD-Score:4.61|P-value:5.05E-6 ID:SGTC_1314|Compound:1222-0010|FD-Score:3.45|P-value:4.65E-4 ID:SGTC_1589|Compound:2',5'-dimethoxyflavone|FD-Score:-3.24|P-value:9.88E-4 ID:SGTC_1631|Compound:benzylvanillin|FD-Score:-4.45|P-value:1.09E-5 ID:SGTC_1637|Compound:st007924|FD-Score:-3.76|P-value:1.69E-4 ID:SGTC_1743|Compound:st037606|FD-Score:3.75|P-value:1.65E-4 ID:SGTC_1876|Compound:myriocin|FD-Score:7.92|P-value:1.64E-14 ID:SGTC_1978|Compound:st071761|FD-Score:-3.34|P-value:7.19E-4 ID:SGTC_2000|Compound:st075254|FD-Score:-3.75|P-value:1.73E-4 ID:SGTC_2010|Compound:4012422|FD-Score:-4.44|P-value:1.13E-5 ID:SGTC_2013|Compound:4024628|FD-Score:4.84|P-value:1.73E-6 ID:SGTC_2020|Compound:4017018|FD-Score:5.59|P-value:4.30E-8 ID:SGTC_2024|Compound:5144227|FD-Score:-7.07|P-value:7.10E-12 ID:SGTC_2045|Compound:5106652|FD-Score:-3.54|P-value:3.64E-4 ID:SGTC_2376|Compound:9072922|FD-Score:3.32|P-value:7.17E-4 ID:SGTC_2567|Compound:aureobasidin a|FD-Score:3.45|P-value:4.64E-4 ID:SGTC_2646|Compound:retinol|FD-Score:3.43|P-value:4.97E-4 ID:SGTC_2678|Compound:equilin|FD-Score:-3.94|P-value:8.63E-5 ID:SGTC_2679|Compound:rapamycin|FD-Score:-3.55|P-value:3.60E-4 ID:SGTC_2804|Compound:7954240|FD-Score:3.94|P-value:7.79E-5 ID:SGTC_2809|Compound:7964133|FD-Score:4.11|P-value:4.15E-5 ID:SGTC_2850|Compound:9015429|FD-Score:3.40|P-value:5.55E-4 ID:SGTC_2853|Compound:9015042|FD-Score:4.09|P-value:4.48E-5 ID:SGTC_2859|Compound:9028643|FD-Score:-4.59|P-value:6.02E-6 ID:SGTC_2959|Compound:9079155|FD-Score:-3.41|P-value:5.77E-4 ID:SGTC_3041|Compound:9091929|FD-Score:3.71|P-value:1.86E-4 ID:SGTC_3173|Compound:9105693|FD-Score:-4.38|P-value:1.49E-5 ID:SGTC_3177|Compound:9107506|FD-Score:-3.29|P-value:8.41E-4 ID:SGTC_3209|Compound:9113616|FD-Score:3.37|P-value:6.06E-4 ID:SGTC_35|Compound:0133-0054|FD-Score:3.90|P-value:9.14E-5 ID:SGTC_37|Compound:0566-0070|FD-Score:3.52|P-value:3.71E-4 ID:SGTC_115|Compound:0527-0192|FD-Score:3.81|P-value:1.32E-4 ID:SGTC_360|Compound:0957-0399|FD-Score:-3.39|P-value:6.15E-4 ID:SGTC_365|Compound:0121-0052|FD-Score:3.96|P-value:7.24E-5 ID:SGTC_369|Compound:0957-0393|FD-Score:3.89|P-value:9.51E-5 ID:SGTC_372|Compound:0155-0182|FD-Score:7.72|P-value:7.25E-14 ID:SGTC_376|Compound:3970-0862|FD-Score:4.23|P-value:2.53E-5 ID:SGTC_457|Compound:grayanotoxin iii|FD-Score:5.22|P-value:2.78E-7 ID:SGTC_528|Compound:3492-0019|FD-Score:5.16|P-value:3.87E-7 ID:SGTC_597|Compound:k018-0003|FD-Score:3.24|P-value:9.36E-4 ID:SGTC_628|Compound:1636-0253|FD-Score:3.65|P-value:2.32E-4 ID:SGTC_671|Compound:0560-0003|FD-Score:5.79|P-value:1.48E-8 ID:SGTC_802|Compound:4112-3352|FD-Score:3.53|P-value:3.55E-4 ID:SGTC_812|Compound:4251-0442|FD-Score:3.92|P-value:8.64E-5 ID:SGTC_866|Compound:0495-0101|FD-Score:4.19|P-value:2.97E-5 ID:SGTC_1215|Compound:3852-0577|FD-Score:-3.69|P-value:2.17E-4 ID:SGTC_1219|Compound:1469-0211|FD-Score:3.67|P-value:2.14E-4 ID:SGTC_1228|Compound:0124-0032|FD-Score:4.61|P-value:5.05E-6 ID:SGTC_1314|Compound:1222-0010|FD-Score:3.45|P-value:4.65E-4 ID:SGTC_1589|Compound:2',5'-dimethoxyflavone|FD-Score:-3.24|P-value:9.88E-4 ID:SGTC_1631|Compound:benzylvanillin|FD-Score:-4.45|P-value:1.09E-5 ID:SGTC_1637|Compound:st007924|FD-Score:-3.76|P-value:1.69E-4 ID:SGTC_1743|Compound:st037606|FD-Score:3.75|P-value:1.65E-4 ID:SGTC_1876|Compound:myriocin|FD-Score:7.92|P-value:1.64E-14 ID:SGTC_1978|Compound:st071761|FD-Score:-3.34|P-value:7.19E-4 ID:SGTC_2000|Compound:st075254|FD-Score:-3.75|P-value:1.73E-4 ID:SGTC_2010|Compound:4012422|FD-Score:-4.44|P-value:1.13E-5 ID:SGTC_2013|Compound:4024628|FD-Score:4.84|P-value:1.73E-6 ID:SGTC_2020|Compound:4017018|FD-Score:5.59|P-value:4.30E-8 ID:SGTC_2024|Compound:5144227|FD-Score:-7.07|P-value:7.10E-12 ID:SGTC_2045|Compound:5106652|FD-Score:-3.54|P-value:3.64E-4 ID:SGTC_2376|Compound:9072922|FD-Score:3.32|P-value:7.17E-4 ID:SGTC_2567|Compound:aureobasidin a|FD-Score:3.45|P-value:4.64E-4 ID:SGTC_2646|Compound:retinol|FD-Score:3.43|P-value:4.97E-4 ID:SGTC_2678|Compound:equilin|FD-Score:-3.94|P-value:8.63E-5 ID:SGTC_2679|Compound:rapamycin|FD-Score:-3.55|P-value:3.60E-4 ID:SGTC_2804|Compound:7954240|FD-Score:3.94|P-value:7.79E-5 ID:SGTC_2809|Compound:7964133|FD-Score:4.11|P-value:4.15E-5 ID:SGTC_2850|Compound:9015429|FD-Score:3.40|P-value:5.55E-4 ID:SGTC_2853|Compound:9015042|FD-Score:4.09|P-value:4.48E-5 ID:SGTC_2859|Compound:9028643|FD-Score:-4.59|P-value:6.02E-6 ID:SGTC_2959|Compound:9079155|FD-Score:-3.41|P-value:5.77E-4 ID:SGTC_3041|Compound:9091929|FD-Score:3.71|P-value:1.86E-4 ID:SGTC_3173|Compound:9105693|FD-Score:-4.38|P-value:1.49E-5 ID:SGTC_3177|Compound:9107506|FD-Score:-3.29|P-value:8.41E-4 ID:SGTC_3209|Compound:9113616|FD-Score:3.37|P-value:6.06E-4

Top fitness defect scores for YDR062W deletion by condition

RankScreen IDConditionFD ScoreConc
P-value
Response
Signature		Screen
Rank
Screen
P-value
Screen
Clearance
1 SGTC_1876 myriocin 7.92 605.0 nM 1.64E-14 2 1.16E-15 0.72
2 SGTC_372 0155-0182 7.72 15.9 µM 7.25E-14 mitochondrial response to ROS 1 5.84E-15 1.27
3 SGTC_671 0560-0003 5.79 407.0 µM 1.48E-8 2 3.57E-9 0.73
4 SGTC_2020 4017018 5.59 200.0 µM 4.30E-8 3 1.14E-8 0.49
5 SGTC_457 grayanotoxin iii 5.22 135.0 µM 2.78E-7 12 8.71E-8 0.04
6 SGTC_528 3492-0019 5.16 172.0 µM 3.87E-7 calcium & mitochondrial duress 13 1.25E-7 0.36
7 SGTC_2013 4024628 4.84 200.0 µM 1.73E-6 4 6.38E-7 0.04
8 SGTC_1228 0124-0032 4.61 52.5 µM 5.05E-6 1 2.04E-6 0.51
9 SGTC_376 3970-0862 4.23 59.1 µM 2.53E-5 6 1.18E-5 0.07
10 SGTC_866 0495-0101 4.19 262.0 µM 2.97E-5 60S ribosome export 6 1.40E-5 0.20
11 SGTC_2809 7964133 4.11 13.0 µM 4.15E-5 60S ribosome export 10 2.02E-5 0.02
12 SGTC_2853 9015042 4.09 58.4 µM 4.48E-5 5 2.19E-5 0.69
13 SGTC_365 0121-0052 3.96 13.6 µM 7.24E-5 mitochondrial response to ROS 7 3.69E-5 0.10
14 SGTC_2804 7954240 3.94 19.5 µM 7.79E-5 11 4.00E-5 0.05
15 SGTC_812 4251-0442 3.92 148.0 µM 8.64E-5 3 4.47E-5 0.06
16 SGTC_35 0133-0054 3.90 64.1 µM 9.14E-5 8 4.76E-5 0.05
17 SGTC_369 0957-0393 3.89 4.5 µM 9.51E-5 cell wall signaling 9 4.96E-5 0.07
18 SGTC_115 0527-0192 3.81 112.0 µM 1.32E-4 27 7.07E-5 0.08
19 SGTC_1743 st037606 3.75 46.4 µM 1.65E-4 9 9.01E-5 0.05
20 SGTC_3041 9091929 3.71 49.5 µM 1.86E-4 redox potentiating 5 1.03E-4 0.30

Download Fitness data (tab-delimited text)  (excel)
Cofit Genes
Download Cofitness data (tab-delimited text)  (excel)

Correlation pval ORF Gene Zygosity Description
0.251 2.13E-49 YMR296C LCB1 het Component of serine palmitoyltransferase, responsible along with Lcb2p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine
0.218 1.62E-37 YGR212W SLI1 hom N-acetyltransferase, confers resistance to the sphingolipid biosynthesis inhibitor myriocin (ISP-1) by converting it into N-acetyl-myriocin, co-operates with Ypk1p in mediating resistance to myriocin
0.142 1.27E-16 YJL134W LCB3 hom Long-chain base-1-phosphate phosphatase; specific for dihydrosphingosine-1-phosphate, regulates ceramide and long-chain base phosphates levels, involved in incorporation of exogenous long chain bases in sphingolipids; LCB3 has a paralog, YSR3, that arose from the whole genome duplication
0.134 7.95E-15 YBR125C PTC4 hom Cytoplasmic type 2C protein phosphatase (PP2C); identified as a high-copy number suppressor of cnb1 mpk1 synthetic lethality; overexpression decreases high-osmolarity induced Hog1p phosphorylation and kinase activity
0.132 2.05E-14 YDR475C JIP4 hom Protein of unknown function; previously annotated as two separate ORFs, YDR474C and YDR475C, which were merged as a result of corrections to the systematic reference sequence
0.130 4.26E-14 YDR071C PAA1 hom Polyamine acetyltransferase; acetylates polyamines (e.g. putrescine, spermidine, spermine) and also aralkylamines (e.g. tryptamine, phenylethylamine); may be involved in transcription and/or DNA replication
0.109 2.15E-10 YJL135W_d YJL135W_d hom Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified genes YJL134W/LCB3
0.087 4.09E-7 YOR269W PAC1 hom Involved in nuclear migration, part of the dynein/dynactin pathway; targets dynein to microtubule tips, which is necessary for sliding of microtubules along bud cortex; serves at interface between dynein's ATPase site and its microtubule binding stalk, causing individual dynein motors to remain attached to microtubules for long periods; synthetic lethal with bni1; homolog of human LIS1, mutations in which cause the severe brain disorder lissencephaly
0.087 4.80E-7 YOR086C TCB1 hom Lipid-binding ER protein involved in ER-plasma membrane tethering; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to the plasma membrane (PM) and regulate PM phosphatidylinositol-4-phosphate (PI4P) levels by controlling access of Sac1p phosphatase to its substrate PI4P in the PM; contains three calcium and lipid binding domains; non-tagged protein also localizes to mitochondria; C-termini of Tcb1p, Tcb2p and Tcb3p interact
0.087 5.04E-7 YDL215C GDH2 hom NAD(+)-dependent glutamate dehydrogenase, degrades glutamate to ammonia and alpha-ketoglutarate; expression sensitive to nitrogen catabolite repression and intracellular ammonia levels
0.085 8.49E-7 YDR098C GRX3 hom Hydroperoxide and superoxide-radical responsive glutathione-dependent oxidoreductase; monothiol glutaredoxin subfamily member along with Grx4p and Grx5p; protects cells from oxidative damage; evidence exists indicating that the translation start site is not Met1 as currently annotated, but rather Met36
0.084 9.78E-7 YDR095C_d YDR095C_d hom Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
0.084 1.02E-6 YGR237C_p YGR237C_p hom Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
0.084 1.10E-6 YDL192W ARF1 hom ADP-ribosylation factor; GTPase of the Ras superfamily involved in regulation of coated vesicle formation in intracellular trafficking within the Golgi; ARF1 has a paralog, ARF2, that arose from the whole genome duplication
0.084 1.13E-6 YGR213C RTA1 hom Protein involved in 7-aminocholesterol resistance; has seven potential membrane-spanning regions; expression is induced under both low-heme and low-oxygen conditions; member of the fungal lipid-translocating exporter (LTE) family of protein