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 SGPP2
Basic gene info.Gene symbolSGPP2
Gene namesphingosine-1-phosphate phosphatase 2
SynonymsSPP2
CytomapUCSC genome browser: 2q36.1
Genomic locationchr2 :223289321-223423617
Type of geneprotein-coding
RefGenesNM_152386.2,
Ensembl idENSG00000163082
DescriptionSPPase2hSPP2sphingosine 1-phosphate phosphohydrolase 2sphingosine-1-phosphatase 2sphingosine-1-phosphate phosphotase 2
Modification date20141207
dbXrefs MIM : 612827
HGNC : HGNC
HPRD : 18048
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SGPP2
BioGPS: 130367
Gene Expression Atlas: ENSG00000163082
The Human Protein Atlas: ENSG00000163082
PathwayNCI Pathway Interaction Database: SGPP2
KEGG: SGPP2
REACTOME: SGPP2
ConsensusPathDB
Pathway Commons: SGPP2
MetabolismMetaCyc: SGPP2
HUMANCyc: SGPP2
RegulationEnsembl's Regulation: ENSG00000163082
miRBase: chr2 :223,289,321-223,423,617
TargetScan: NM_152386
cisRED: ENSG00000163082
ContextiHOP: SGPP2
cancer metabolism search in PubMed: SGPP2
UCL Cancer Institute: SGPP2
Assigned class in ccmGDBC

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Phenotypic Information for SGPP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SGPP2
Familial Cancer Database: SGPP2
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SGPP2
MedGen: SGPP2 (Human Medical Genetics with Condition)
ClinVar: SGPP2
PhenotypeMGI: SGPP2 (International Mouse Phenotyping Consortium)
PhenomicDB: SGPP2

Mutations for SGPP2
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSGPP2chr2223365892223365912SGPP2chr2223366373223366393
pancreasSGPP2chr2223370847223370867SGPP2chr2223367866223367886
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SGPP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW847114SGPP231162223298432223298545FAM13A11338648967355089673824

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     1 1        
GAIN (# sample)        1        
LOSS (# sample)1     1          
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr2:223339308-223339308p.V81M3
chr2:223386549-223386549p.P148S3
chr2:223386613-223386613p.A169V3
chr2:223423423-223423423p.L336F2
chr2:223423432-223423432p.R339C2
chr2:223423433-223423433p.R339H2
chr2:223389736-223389736p.G211E2
chr2:223339442-223339442p.W125C1
chr2:223389666-223389666p.P188S1
chr2:223289522-223289522p.R67R1

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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
# sample31152   4   11  71 5
# mutation31162   4   11  91 5
nonsynonymous SNV11 52   4    1  71 5
synonymous SNV2 11        1   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
chr2:223339308p.V81M2
chr2:223386613p.A169V2
chr2:223386573p.V80I1
chr2:223423168p.L193M1
chr2:223339305p.R359M1
chr2:223423493p.L205L1
chr2:223386575p.F92L1
chr2:223423243p.D240N1
chr2:223386606p.G97V1
chr2:223423285p.A245T1

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 SGPP2 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 SGPP2

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

ACSBG1,AKR1B15,AKR1D1,ACTRT3,B3GAT1,C6orf223,CHRNB4,
FCN2,GUSB,ESRG,IDH1,IDI1,ISX,MYNN,
MYOM2,PNLIPRP3,RLN3,RNASE11,RNASE12,SGPP2,SRD5A1
ABCC12,ACSL3,ADCY10,AKR1D1,ALOX15B,C15orf43,CTNNA2,
ELOVL7,EPS8L3,FMO5,HIST1H2AG,IDI1,IYD,LST-3TM12,
NSUN2,SERHL,SGPP2,SLC12A3,SLC26A6,TMPRSS11F,ZP2

MYRF,GDPGP1,CASP10,CCDC68,CDCP1,RHOV___CHP1,DOCK5,
LIMA1,LIPH,PFKP,PLXNB2,RAB27B,RNF19B,SGPP2,
SHROOM3,SLC1A1,SLC37A1,SLC41A2,SOCS6,UGT8,VPS4B
CAPN5,CDH1,DNM2,ELF4,ERBB3,HNF4A,JUP,
KIAA1522,LSR,MARK2,NR3C2,OCLN,PCDH1,PEX26,
RAB11FIP1,SCAMP2,SGPP2,ST14,TJP3,TMEM170A,WWP2
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 SGPP2


There's no related Drug.
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Cross referenced IDs for SGPP2
* 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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