mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for SPHK1
Gene summary
Basic gene Info.Gene symbolSPHK1
Gene namesphingosine kinase 1
SynonymsSPHK
CytomapUCSC genome browser: 17q25.2
Type of geneprotein-coding
RefGenesNM_001142601.1,
NM_001142602.1,NM_021972.3,NM_182965.2,
DescriptionSK 1SPK 1
Modification date20141222
dbXrefs MIM : 603730
HGNC : HGNC
Ensembl : ENSG00000176170
HPRD : 04768
Vega : OTTHUMG00000180177
ProteinUniProt: Q9NYA1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SPHK1
BioGPS: 8877
PathwayNCI Pathway Interaction Database: SPHK1
KEGG: SPHK1
REACTOME: SPHK1
Pathway Commons: SPHK1
ContextiHOP: SPHK1
ligand binding site mutation search in PubMed: SPHK1
UCL Cancer Institute: SPHK1
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006670sphingosine metabolic process20577214
GO:0010803regulation of tumor necrosis factor-mediated signaling pathway20577214
GO:0019722calcium-mediated signaling10947957
GO:0030307positive regulation of cell growth12441135
GO:0030335positive regulation of cell migration12441135
GO:0031398positive regulation of protein ubiquitination20577214
GO:0043066negative regulation of apoptotic process15623571
GO:0045766positive regulation of angiogenesis12441135
GO:0045931positive regulation of mitotic cell cycle12441135
GO:0045987positive regulation of smooth muscle contraction12847068
GO:0046834lipid phosphorylation12393916
GO:0048146positive regulation of fibroblast proliferation15623571


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Ligand binding site mutations for SPHK1
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 : non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
L302R301PCOAD1
E343M345ISKCM1
G113A115TSTAD1
S168A170TSTAD1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for SPHK1
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
S168A170T-1.4035756
L302R301P-0.88746247
E343M345I-0.31562965
G113A115T-0.050300328
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for SPHK1 from PDB

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Differential gene expression and gene-gene network for SPHK1
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of SPHK1 and the right PPI network was created from samples without mutations in the LBS of SPHK1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for SPHK1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023418Leukemia3Biomarker
umls:C0016059Fibrosis1Therapeutic
umls:C0026986Myelodysplastic Syndromes1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for SPHK1
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SPHK1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
MGMAGNESIUM(2+)3vzdBE343
MGMAGNESIUM(2+)3vzdCE343
MGMAGNESIUM(2+)3vzdEE343
POPDIPHOSPHATE(2-)3vzdBG113
ADPADP3vzdCG113 E343
ADPADP3vzdEG113 E343
SQSD-SPHINGOSINE(2S,3R,4E)-2-AMINOOCTADEC-4-ENE-1,3-DIOL3vzbAS168
SQSD-SPHINGOSINE(2S,3R,4E)-2-AMINOOCTADEC-4-ENE-1,3-DIOL3vzbBS168
1V2(2R,4S)-1-[2-(4-{[4-(3,4-DICHLOROPHENYL)-1,3-THIAZOL-2- YL]AMINO}PHENYL)ETHYL]-2-(HYDROXYMETHYL)PIPERIDIN-4-OL4l02AS168
1V2(2R,4S)-1-[2-(4-{[4-(3,4-DICHLOROPHENYL)-1,3-THIAZOL-2- YL]AMINO}PHENYL)ETHYL]-2-(HYDROXYMETHYL)PIPERIDIN-4-OL4l02BS168
1V2(2R,4S)-1-[2-(4-{[4-(3,4-DICHLOROPHENYL)-1,3-THIAZOL-2- YL]AMINO}PHENYL)ETHYL]-2-(HYDROXYMETHYL)PIPERIDIN-4-OL4l02CS168


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Conservation information for LBS of SPHK1
Multiple alignments for Q9NYA1 in multiple species
LBSAA sequence# speciesSpecies
A201TFFRLASLRIY2Mus musculus, Rattus norvegicus
A201TFLRLAALRTY1Homo sapiens
A274GSEMFAAPMGR1Homo sapiens
A274SSELFAAPMGR1Mus musculus
A274STEMFAAPMGR1Rattus norvegicus
A297AGVSRAMLLRL1Homo sapiens
A297AGVSRAALLRL1Mus musculus
A297AGVSRAMLVRL1Rattus norvegicus
A339QRGVFSVDGEL2Mus musculus, Rattus norvegicus
A339GKGVFAVDGEL1Homo sapiens
D178FVADVDLESEK2Mus musculus, Rattus norvegicus
D178FIADVDLESEK1Homo sapiens
D341GVFSVDGELMV2Mus musculus, Rattus norvegicus
D341GVFAVDGELMV1Homo sapiens
D81AVMSGDGLMHE2Mus musculus, Rattus norvegicus
D81VVMSGDGLMHE1Homo sapiens
E343FSVDGELMVCE2Mus musculus, Rattus norvegicus
E343FAVDGELMVSE1Homo sapiens
E55TLMLTERRNHA1Homo sapiens
E55KLILTERKNHA1Mus musculus
E55KLMLTERQNHA1Rattus norvegicus
E86DGLMHEVVNGL3Homo sapiens, Mus musculus, Rattus norvegicus
F173SLSWGFVADVD2Mus musculus, Rattus norvegicus
F173SLAWGFIADVD1Homo sapiens
F192LGEIRFTVGTF2Mus musculus, Rattus norvegicus
F192LGEMRFTLGTF1Homo sapiens
F197FTVGTFFRLAS2Mus musculus, Rattus norvegicus
F197FTLGTFLRLAA1Homo sapiens
F288GVMHLFYVRAG2Homo sapiens, Mus musculus
F288GVMHLFYIRAG1Rattus norvegicus
F303MLLRLFLAMEK1Homo sapiens
F303ALLRLFLAMQK1Mus musculus
F303MLVRLFLAMQK1Rattus norvegicus
G111CSLPGGSGNAL2Mus musculus, Rattus norvegicus
G111CSLPAGSGNAL1Homo sapiens
G113LPGGSGNALAA2Mus musculus, Rattus norvegicus
G113LPAGSGNALAA1Homo sapiens
G342VFSVDGELMVC2Mus musculus, Rattus norvegicus
G342VFAVDGELMVS1Homo sapiens
G80LAVMSGDGLMH2Mus musculus, Rattus norvegicus
G80LVVMSGDGLMH1Homo sapiens
G82VMSGDGLMHEV3Homo sapiens, Mus musculus, Rattus norvegicus
H311MEKGRHMEYEC1Homo sapiens
H311MQKGKHMELDC1Mus musculus
H311MQKGKHMDLDC1Rattus norvegicus
I174LSWGFVADVDL2Mus musculus, Rattus norvegicus
I174LAWGFIADVDL1Homo sapiens
L167RLFSVLSLAWG1Homo sapiens
L167RLYSVLSLSWG1Mus musculus
L167QLYSVLSLSWG1Rattus norvegicus
L200GTFFRLASLRI2Mus musculus, Rattus norvegicus
L200GTFLRLAALRT1Homo sapiens
L259EQDFVLVLVLL2Mus musculus, Rattus norvegicus
L259DEDFVLVLALL1Homo sapiens
L261DFVLVLVLLHT2Mus musculus, Rattus norvegicus
L261DFVLVLALLHS1Homo sapiens
L268LLHSHLGSEMF1Homo sapiens
L268LLHTHLSSELF1Mus musculus
L268LLHTHLSTEMF1Rattus norvegicus
L299VSRAMLLRLFL1Homo sapiens
L299VSRAALLRLFL1Mus musculus
L299VSRAMLVRLFL1Rattus norvegicus
L302AMLLRLFLAME1Homo sapiens
L302AALLRLFLAMQ1Mus musculus
L302AMLVRLFLAMQ1Rattus norvegicus
L319LDCPYLVHVPV2Mus musculus, Rattus norvegicus
L319YECPYLVYVPV1Homo sapiens
L83MSGDGLMHEVV3Homo sapiens, Mus musculus, Rattus norvegicus
M272HLGSEMFAAPM1Homo sapiens
M272HLSSELFAAPM1Mus musculus
M272HLSTEMFAAPM1Rattus norvegicus
M306RLFLAMQKGKH2Mus musculus, Rattus norvegicus
M306RLFLAMEKGRH1Homo sapiens
N22VLVLLNPRGGK2Homo sapiens, Rattus norvegicus
N22VLVLLNPQGGK1Mus musculus
R185ESEKYRRLGEM1Homo sapiens
R185ESEKYRRLGEI1Mus musculus
R185ESEKYRSLGEI1Rattus norvegicus
R191RLGEMRFTLGT1Homo sapiens
R191RLGEIRFTVGT1Mus musculus
R191SLGEIRFTVGT1Rattus norvegicus
R24VLLNPRGGKGK2Homo sapiens, Rattus norvegicus
R24VLLNPQGGKGK1Mus musculus
R296RAGVSRAMLLR1Homo sapiens
R296RAGVSRAALLR1Mus musculus
R296RAGVSRAMLVR1Rattus norvegicus
R56LMLTERRNHAR1Homo sapiens
R56LILTERKNHAR1Mus musculus
R56LMLTERQNHAR1Rattus norvegicus
S112SLPGGSGNALA2Mus musculus, Rattus norvegicus
S112SLPAGSGNALA1Homo sapiens
S168LYSVLSLSWGF2Mus musculus, Rattus norvegicus
S168LFSVLSLAWGF1Homo sapiens
S79ALAVMSGDGLM2Mus musculus, Rattus norvegicus
S79ALVVMSGDGLM1Homo sapiens
T196RFTVGTFFRLA2Mus musculus, Rattus norvegicus
T196RFTLGTFLRLA1Homo sapiens
T54FTLMLTERRNH1Homo sapiens
T54FKLILTERKNH1Mus musculus
T54FKLMLTERQNH1Rattus norvegicus
V177GFVADVDLESE2Mus musculus, Rattus norvegicus
V177GFIADVDLESE1Homo sapiens


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