Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for SPHK2
Basic gene info.Gene symbolSPHK2
Gene namesphingosine kinase 2
SynonymsSK 2|SK-2|SPK 2|SPK-2
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :49122547-49133663
Type of geneprotein-coding
RefGenesNM_001204158.2,
NM_001204159.2,NM_001204160.2,NM_001243876.1,NM_020126.4,
Ensembl idENSG00000063176
Descriptionsphingosine kinase type 2
Modification date20141207
dbXrefs MIM : 607092
HGNC : HGNC
Ensembl : ENSG00000063176
HPRD : 06157
Vega : OTTHUMG00000183318
ProteinUniProt: Q9NRA0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SPHK2
BioGPS: 56848
Gene Expression Atlas: ENSG00000063176
The Human Protein Atlas: ENSG00000063176
PathwayNCI Pathway Interaction Database: SPHK2
KEGG: SPHK2
REACTOME: SPHK2
ConsensusPathDB
Pathway Commons: SPHK2
MetabolismMetaCyc: SPHK2
HUMANCyc: SPHK2
RegulationEnsembl's Regulation: ENSG00000063176
miRBase: chr19 :49,122,547-49,133,663
TargetScan: NM_001204158
cisRED: ENSG00000063176
ContextiHOP: SPHK2
cancer metabolism search in PubMed: SPHK2
UCL Cancer Institute: SPHK2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SPHK2 in cancer cell metabolism1. 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)
check002.gifCancer Description
Cancer CGAP: SPHK2
Familial Cancer Database: SPHK2
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_SPHINGOLIPID_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 607092; gene.
Orphanet
DiseaseKEGG Disease: SPHK2
MedGen: SPHK2 (Human Medical Genetics with Condition)
ClinVar: SPHK2
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SPHK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
C02583MAP1A1166154381485643815229SPHK2163317194913350849133661

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:49132881-49132881p.R606C3
chr19:49132634-49132634p.L523L3
chr19:49129486-49129486p.G126G3
chr19:49131042-49131042p.N202S2
chr19:49132338-49132338p.L425F2
chr19:49132104-49132104p.S347G2
chr19:49131491-49131491p.G277S2
chr19:49123805-49123805p.D12N2
chr19:49132383-49132383p.P440T2
chr19:49131947-49131947p.P294P2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample43152 2 2  22   103 5
# mutation53152 2 2  22   103 5
nonsynonymous SNV32 4  1 1  21   71 3
synonymous SNV21112 1 1   1   32 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:49132307p.S378S,SPHK22
chr19:49132338p.L389V,SPHK22
chr19:49132082p.P13S,SPHK21
chr19:49132515p.R274W,SPHK21
chr19:49131293p.P486L,SPHK21
chr19:49132111p.G17G,SPHK21
chr19:49129225p.L280L,SPHK21
chr19:49132520p.S537S,SPHK21
chr19:49131440p.R44H,SPHK21
chr19:49132129p.R292C,SPHK21

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for SPHK2 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 SPHK2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for SPHK2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q9NRA0; -.
ChemistryChEMBL CHEMBL3023; -.
ChemistryGuidetoPHARMACOLOGY 2205; -.
Organism-specific databasesPharmGKB PA38719; -.
Organism-specific databasesCTD 56848; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00143sphingosine kinase 2approved; nutraceuticalGlutathione


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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

: Open all cross reference information



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