Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SGPP1
Basic gene info.Gene symbolSGPP1
Gene namesphingosine-1-phosphate phosphatase 1
SynonymsSPPase1
CytomapUCSC genome browser: 14q23.2
Genomic locationchr14 :64150934-64194756
Type of geneprotein-coding
RefGenesNM_030791.2,
Ensembl idENSG00000126821
DescriptionhSPP1hSPPase1sphingosine-1-phosphatase 1spp1
Modification date20141211
dbXrefs MIM : 612826
HGNC : HGNC
Ensembl : ENSG00000126821
HPRD : 10226
Vega : OTTHUMG00000029080
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SGPP1
BioGPS: 81537
Gene Expression Atlas: ENSG00000126821
The Human Protein Atlas: ENSG00000126821
PathwayNCI Pathway Interaction Database: SGPP1
KEGG: SGPP1
REACTOME: SGPP1
ConsensusPathDB
Pathway Commons: SGPP1
MetabolismMetaCyc: SGPP1
HUMANCyc: SGPP1
RegulationEnsembl's Regulation: ENSG00000126821
miRBase: chr14 :64,150,934-64,194,756
TargetScan: NM_030791
cisRED: ENSG00000126821
ContextiHOP: SGPP1
cancer metabolism search in PubMed: SGPP1
UCL Cancer Institute: SGPP1
Assigned class in ccmGDBC

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Phenotypic Information for SGPP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SGPP1
Familial Cancer Database: SGPP1
* 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: SGPP1
MedGen: SGPP1 (Human Medical Genetics with Condition)
ClinVar: SGPP1
PhenotypeMGI: SGPP1 (International Mouse Phenotyping Consortium)
PhenomicDB: SGPP1

Mutations for SGPP1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSGPP1chr146416099664161016chr224770456147704581
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 SGPP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=26)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr14:64152941-64152941p.R403Q3
chr14:64153205-64153205p.S315F2
chr14:64194115-64194115p.W183S2
chr14:64153098-64153098p.P351S2
chr14:64152863-64152863p.F429C1
chr14:64194508-64194508p.D52A1
chr14:64153112-64153112p.S346C1
chr14:64194048-64194048p.P205P1
chr14:64152902-64152902p.R416P1
chr14:64153129-64153129p.G340G1

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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
# sample11 7  2 2  211   1 4
# mutation11 7  2 2  211   1 4
nonsynonymous SNV 1 6  2 2  211   1 2
synonymous SNV1  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
chr14:64152941p.R403Q2
chr14:64153098p.P351S2
chr14:64152887p.G421V1
chr14:64153129p.P189T1
chr14:64152902p.R416P1
chr14:64153328p.M171T1
chr14:64152913p.E412D1
chr14:64153364p.L142L1
chr14:64193979p.L390F1
chr14:64152979p.V374L1

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 SGPP1 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 SGPP1

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

GSKIP,CNIH1,DTWD2,GMFB,ITM2B,MAPK1IP1L,MGAT2,
NAA30,NR3C1,PCGF5,PPP2R5E,RP2,SEC24A,SEL1L,
SGPP1,SNAP23,TMED10,TMED7,TMEM87B,WDR89,ZBTB1
ACTR2,CHUK,CLIC4,DYNLT3,ERI1,EVI5,GMFB,
GOLT1B,BLOC1S6,PLEKHA3,RAB8B,RAP1B,SGMS1,SGPP1,
SHOC2,SOCS4,TMEM167A,TMX3,TROVE2,UBL3,VAMP7

ACER3,ARF6,EXD2,EXOC5,FBXO33,GCH1,HIF1A,
JKAMP,MAPK1IP1L,PDE4D,PPM1A,RAB27A,SCFD1,SGPP1,
SNX6,STRN3,STYX,TMED10,TMX1,TRAPPC6B,TWSG1
ARPC5L,CASP9,CHUK,DDX52,DNTTIP2,ELL2,FAM107B,
LSM12,MAP2K4,MAT2A,NIP7,PIGA,POLD3,RB1,
SERTAD1,SRSF2,SGPP1,TAF5L,TDG,UAP1,WTAP
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 SGPP1


There's no related Drug.
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Cross referenced IDs for SGPP1
* 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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