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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SPHK2 |
Basic gene info. | Gene symbol | SPHK2 |
Gene name | sphingosine kinase 2 | |
Synonyms | SK 2|SK-2|SPK 2|SPK-2 | |
Cytomap | UCSC genome browser: 19q13.2 | |
Genomic location | chr19 :49122547-49133663 | |
Type of gene | protein-coding | |
RefGenes | NM_001204158.2, NM_001204159.2,NM_001204160.2,NM_001243876.1,NM_020126.4, | |
Ensembl id | ENSG00000063176 | |
Description | sphingosine kinase type 2 | |
Modification date | 20141207 | |
dbXrefs | MIM : 607092 | |
HGNC : HGNC | ||
Ensembl : ENSG00000063176 | ||
HPRD : 06157 | ||
Vega : OTTHUMG00000183318 | ||
Protein | UniProt: Q9NRA0 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SPHK2 | |
BioGPS: 56848 | ||
Gene Expression Atlas: ENSG00000063176 | ||
The Human Protein Atlas: ENSG00000063176 | ||
Pathway | NCI Pathway Interaction Database: SPHK2 | |
KEGG: SPHK2 | ||
REACTOME: SPHK2 | ||
ConsensusPathDB | ||
Pathway Commons: SPHK2 | ||
Metabolism | MetaCyc: SPHK2 | |
HUMANCyc: SPHK2 | ||
Regulation | Ensembl's Regulation: ENSG00000063176 | |
miRBase: chr19 :49,122,547-49,133,663 | ||
TargetScan: NM_001204158 | ||
cisRED: ENSG00000063176 | ||
Context | iHOP: SPHK2 | |
cancer metabolism search in PubMed: SPHK2 | ||
UCL Cancer Institute: SPHK2 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of SPHK2 in cancer cell metabolism | 1. Engel N, Lisec J, Piechulla B, Nebe B (2012) Metabolic profiling reveals sphingosine-1-phosphate kinase 2 and lyase as key targets of (phyto-) estrogen action in the breast cancer cell line mcf-7 and not in mcf-12a. go to article 2. Degagné E, Saba JD (2014) S1pping fire: Sphingosine-1-phosphate signaling as an emerging target in inflammatory bowel disease and colitis-associated cancer. Clinical and experimental gastroenterology 7: 205. go to article |
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Phenotypic Information for SPHK2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SPHK2 |
Familial Cancer Database: SPHK2 |
* 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/ |
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KEGG_SPHINGOLIPID_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | 607092; gene. |
Orphanet | |
Disease | KEGG Disease: SPHK2 |
MedGen: SPHK2 (Human Medical Genetics with Condition) | |
ClinVar: SPHK2 | |
Phenotype | MGI: SPHK2 (International Mouse Phenotyping Consortium) |
PhenomicDB: SPHK2 |
Mutations for SPHK2 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SPHK2 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 |
C02583 | MAP1A | 1 | 166 | 15 | 43814856 | 43815229 | SPHK2 | 163 | 317 | 19 | 49133508 | 49133661 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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Stat. for Non-Synonymous SNVs (# total SNVs=42) | (# total SNVs=18) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr19:49132881-49132881 | p.R606C | 3 |
chr19:49132634-49132634 | p.L523L | 3 |
chr19:49129486-49129486 | p.G126G | 3 |
chr19:49131011-49131011 | p.G192C | 2 |
chr19:49131440-49131440 | p.R260C | 2 |
chr19:49132331-49132331 | p.D422E | 2 |
chr19:49131453-49131453 | p.E264V | 2 |
chr19:49132338-49132338 | p.L425F | 2 |
chr19:49131042-49131042 | p.N202S | 2 |
chr19:49132104-49132104 | p.S347G | 2 |
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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 | 4 | 3 | 1 | 5 | 2 |   | 2 |   | 2 |   |   | 2 | 2 |   |   |   | 10 | 3 |   | 5 |
# mutation | 5 | 3 | 1 | 5 | 2 |   | 2 |   | 2 |   |   | 2 | 2 |   |   |   | 10 | 3 |   | 5 |
nonsynonymous SNV | 3 | 2 |   | 4 |   |   | 1 |   | 1 |   |   | 2 | 1 |   |   |   | 7 | 1 |   | 3 |
synonymous SNV | 2 | 1 | 1 | 1 | 2 |   | 1 |   | 1 |   |   |   | 1 |   |   |   | 3 | 2 |   | 2 |
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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* 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 |
chr19:49132307 | p.S378S,SPHK2 | 2 |
chr19:49132338 | p.L389V,SPHK2 | 2 |
chr19:49132013 | p.E60K,SPHK2 | 1 |
chr19:49132455 | p.S319T,SPHK2 | 1 |
chr19:49131265 | p.A571A,SPHK2 | 1 |
chr19:49132047 | p.V194V,SPHK2 | 1 |
chr19:49132505 | p.L330L,SPHK2 | 1 |
chr19:49131269 | p.G581G,SPHK2 | 1 |
chr19:49132082 | p.G196E,SPHK2 | 1 |
chr19:49132515 | p.Y342S,SPHK2 | 1 |
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* 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. |
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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 SPHK2 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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ARMC5,BBC3,TMEM259,CAPN10,CCDC9,CROCC,CYTH2, FLYWCH1,GLTSCR1,IRF2BP1,MIB2,MZF1,PNKP,PPP1R12C, RHOT2,SNRNP70,SPHK2,SPSB3,TBC1D17,ZNF205,ZNF628 | AAMP,ARFRP1,BRF1,ST20-AS1,BRAT1,NELFB,FAM73B, GTF2H4,HDGFRP2,HGS,PEX16,PFKL,PNKP,SCAF1, SELO,SIX5,SPHK2,SPSB3,TAF6L,TELO2,WDR83 | ||||
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B3GNT8,CYP2B6,DHX34,ENGASE,EPN1,FBXO46,GLTSCR1, HNF1A,NAPA,NR1I2,PPP2R1A,PRR12,SCAF1,SGK2, SLC39A5,SPHK2,SYMPK,VIL1,ZBTB45,ZNF526,ZNF787 | ACADS,ACSF3,BAIAP2L2,CEBPA,DAPK2,DHRS11,DOLPP1, ESPN,FAM73B,HECTD3,LPCAT3,MAP2K2,MGAT4B,PLEKHG6, PPAP2C,PPP1R16A,RAB40C,SPHK2,SPINT1,ULK3,ZBTB7B |
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* 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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Pharmacological Information for SPHK2 |
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DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | Q9NRA0; -. |
Chemistry | ChEMBL | CHEMBL3023; -. |
Chemistry | GuidetoPHARMACOLOGY | 2205; -. |
Organism-specific databases | PharmGKB | PA38719; -. |
Organism-specific databases | CTD | 56848; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00143 | sphingosine kinase 2 | approved; nutraceutical | Glutathione | ![]() | ![]() |
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Cross referenced IDs for SPHK2 |
* 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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