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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SPHK1 |
Basic gene info. | Gene symbol | SPHK1 |
Gene name | sphingosine kinase 1 | |
Synonyms | SPHK | |
Cytomap | UCSC genome browser: 17q25.2 | |
Genomic location | chr17 :74380689-74383941 | |
Type of gene | protein-coding | |
RefGenes | NM_001142601.1, NM_001142602.1,NM_021972.3,NM_182965.2, | |
Ensembl id | ENSG00000176170 | |
Description | SK 1SPK 1 | |
Modification date | 20141222 | |
dbXrefs | MIM : 603730 | |
HGNC : HGNC | ||
Ensembl : ENSG00000176170 | ||
HPRD : 04768 | ||
Vega : OTTHUMG00000180177 | ||
Protein | UniProt: Q9NYA1 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SPHK1 | |
BioGPS: 8877 | ||
Gene Expression Atlas: ENSG00000176170 | ||
The Human Protein Atlas: ENSG00000176170 | ||
Pathway | NCI Pathway Interaction Database: SPHK1 | |
KEGG: SPHK1 | ||
REACTOME: SPHK1 | ||
ConsensusPathDB | ||
Pathway Commons: SPHK1 | ||
Metabolism | MetaCyc: SPHK1 | |
HUMANCyc: SPHK1 | ||
Regulation | Ensembl's Regulation: ENSG00000176170 | |
miRBase: chr17 :74,380,689-74,383,941 | ||
TargetScan: NM_001142601 | ||
cisRED: ENSG00000176170 | ||
Context | iHOP: SPHK1 | |
cancer metabolism search in PubMed: SPHK1 | ||
UCL Cancer Institute: SPHK1 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of SPHK1 in cancer cell metabolism | 1. Guillermet-Guibert J, Davenne L, Pchejetski D, Saint-Laurent N, Brizuela L, et al. (2009) Targeting the sphingolipid metabolism to defeat pancreatic cancer cell resistance to the chemotherapeutic gemcitabine drug. Molecular cancer therapeutics 8: 809-820. go to article 2. Tamashiro PM, Furuya H, Shimizu Y, Iino K, Kawamori T (2013) The impact of sphingosine kinase-1 in head and neck cancer. Biomolecules 3: 481-513. go to article |
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Phenotypic Information for SPHK1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SPHK1 |
Familial Cancer Database: SPHK1 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
KEGG_SPHINGOLIPID_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_PROTEINS REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | 603730; gene. |
Orphanet | |
Disease | KEGG Disease: SPHK1 |
MedGen: SPHK1 (Human Medical Genetics with Condition) | |
ClinVar: SPHK1 | |
Phenotype | MGI: SPHK1 (International Mouse Phenotyping Consortium) |
PhenomicDB: SPHK1 |
Mutations for SPHK1 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SPHK1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
CA426947 | SPHK1 | 8 | 383 | 17 | 74377604 | 74377979 | SPHK1 | 375 | 712 | 17 | 74377210 | 74377546 | |
BF915954 | SPHK1 | 1 | 141 | 17 | 74383792 | 74383932 | EP300 | 139 | 289 | 22 | 41574556 | 41574706 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=43) | (# total SNVs=8) |
(# total SNVs=2) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr17:74381567-74381567 | p.A34T | 13 |
chr17:74381555-74381555 | p.A30T | 11 |
chr17:74382331-74382331 | p.R151W | 2 |
chr17:74382405-74382405 | p.? | 2 |
chr17:74382586-74382586 | p.A210D | 2 |
chr17:74383582-74383582 | p.N443S | 2 |
chr17:74383376-74383376 | p.F374L | 2 |
chr17:74382172-74382172 | p.Q125H | 1 |
chr17:74383602-74383602 | p.G450S | 1 |
chr17:74382930-74382930 | p.L226L | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   | 1 | 3 |   |   |   |   |   | 1 |   | 3 | 1 | 1 |   |   | 1 | 6 | 1 | 3 |
# mutation |   |   | 1 | 3 |   |   |   |   |   | 1 |   | 3 | 1 | 1 |   |   | 1 | 6 | 1 | 3 |
nonsynonymous SNV |   |   | 1 | 1 |   |   |   |   |   | 1 |   |   |   | 1 |   |   | 1 | 6 |   | 2 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   | 3 | 1 |   |   |   |   |   | 1 | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr17:74382929 | p.R145R,SPHK1 | 1 |
chr17:74383414 | p.L147L,SPHK1 | 1 |
chr17:74382930 | p.T157A,SPHK1 | 1 |
chr17:74383472 | p.A170T,SPHK1 | 1 |
chr17:74382931 | p.G216G,SPHK1 | 1 |
chr17:74383547 | p.D235H,SPHK1 | 1 |
chr17:74382947 | p.P253A,SPHK1 | 1 |
chr17:74383634 | p.K27E,SPHK1 | 1 |
chr17:74382953 | p.A292V,SPHK1 | 1 |
chr17:74382134 | p.G28D,SPHK1 | 1 |
Other DBs for Point Mutations |
Copy Number for SPHK1 in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, 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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Gene Expression for SPHK1 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
BATF3,BMP1,FHL3,KIF7,KIFC3,LGALS1,LMNA, MFAP2,MIIP,NXN,PDLIM7,PLEKHO1,PLSCR3,POLR2F, PRKCDBP,QRICH2,SERPINH1,SMTN,SPHK1,TPM2,TUBB6 | ARID5A,ARMC5,BAX,C11orf84,CDC42EP1,ERF,FAM129B, GPSM1,GRK6,IL27RA,IL34,KLF16,AGAP2-AS1,PDLIM4, PLEKHA4,PUS1,SFN,SPATA2L,SPHK1,THOC6,VASP |
ARSI,CALHM2,CD14,CD86,CERCAM,DPYD,FCER1G, FCGR3A,GPR68,HAPLN3,HAVCR2,MAFB,MMP14,PDCD1LG2, PILRA,PMP22,PRRX1,RCN3,SERPINH1,SPHK1,TGFB1 | ACHE,ADRM1,ARPC1B,C4BPA,CD164L2,CHRM4,HYPM, DUOXA1,ENKUR,FHL2,HIST1H2BC,IL3RA,PCBP1,PLIN3, RHOG,SFTA2,SLC17A3,SPHK1,SPNS2,SURF4,TRIM40 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for SPHK1 |
There's no related Drug. |
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Cross referenced IDs for SPHK1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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