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 SEPHS2
Basic gene info.Gene symbolSEPHS2
Gene nameselenophosphate synthetase 2
SynonymsSPS2|SPS2b
CytomapUCSC genome browser: 16p11.2
Genomic locationchr16 :30454951-30457224
Type of geneprotein-coding
RefGenesNM_012248.3,
Ensembl idENSG00000179918
Descriptionselenide, water dikinase 2selenium donor protein 2selenophosphate synthase 2
Modification date20141207
dbXrefs MIM : 606218
HGNC : HGNC
Ensembl : ENSG00000179918
HPRD : 12096
Vega : OTTHUMG00000176988
ProteinUniProt: Q99611
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEPHS2
BioGPS: 22928
Gene Expression Atlas: ENSG00000179918
The Human Protein Atlas: ENSG00000179918
PathwayNCI Pathway Interaction Database: SEPHS2
KEGG: SEPHS2
REACTOME: SEPHS2
ConsensusPathDB
Pathway Commons: SEPHS2
MetabolismMetaCyc: SEPHS2
HUMANCyc: SEPHS2
RegulationEnsembl's Regulation: ENSG00000179918
miRBase: chr16 :30,454,951-30,457,224
TargetScan: NM_012248
cisRED: ENSG00000179918
ContextiHOP: SEPHS2
cancer metabolism search in PubMed: SEPHS2
UCL Cancer Institute: SEPHS2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SEPHS2 in cancer cell metabolism1. Dudaladava V, Jarząb M, Stobiecka E, Chmielik E, Simek K, et al. (2006) Gene expression profiling in hereditary, BRCA1-linked breast cancer: preliminary report. Hered Cancer Clin Pract 4: 28. go to article

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Phenotypic Information for SEPHS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEPHS2
Familial Cancer Database: SEPHS2
* 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_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM 606218; gene.
Orphanet
DiseaseKEGG Disease: SEPHS2
MedGen: SEPHS2 (Human Medical Genetics with Condition)
ClinVar: SEPHS2
PhenotypeMGI: SEPHS2 (International Mouse Phenotyping Consortium)
PhenomicDB: SEPHS2

Mutations for SEPHS2
* 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 SEPHS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA344463CRP11901159683023159683212SEPHS2186276163045628630456377

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
There's no copy number variation information in COSMIC data for this gene.

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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=26)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr16:30455863-30455863p.G396R3
chr16:30456542-30456542p.E169E2
chr16:30456293-30456293p.K252N2
chr16:30456698-30456698p.I117I2
chr16:30456699-30456699p.I117T2
chr16:30455847-30455847p.A401V1
chr16:30456114-30456114p.H312R1
chr16:30456484-30456484p.E189K1
chr16:30455759-30455759p.A430A1
chr16:30456144-30456144p.A302D1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 SEPHS2 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 SEPHS2

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

ALDOA,ALG1,BCKDK,KNOP1,CD2BP2,CLN3,DCTPP1,
DNAJA3,EARS2,FAHD1,HN1L,MAPK3,NDUFAB1,POLR3K,
PPP4C,RNF40,SEPHS2,USP7,ZNF747,ZNF764,ZNF768
ACSS1,APOF,ASCL2,ATP6AP1,ATP6V1H,C2orf54,RHPN1-AS1,
CALML5,CYP4F2,FAM110A,GALNTL6,HMX2,KLHL35,CERS4,
MAPK8IP2,PDCL3,PYY,SLC50A1,SEPHS2,SLC7A13,SQLE

ACOT8,CD2BP2,CHMP4B,CTSA,CYB5B,DCTPP1,DNAJA3,
FAM192A,FBRS,MYLPF,PAPD5,PRR14,PUS10,PXMP4,
QPRT,SEPHS2,SLMO2,TBC1D10B,ZNF747,ZNF768,ZSWIM3
ABHD12,ACSL5,ANKS4B,LINC00483,LRRC75A,C1orf115,CLRN3,
DCAF11,DHRS11,ESPN,FMO4,GDPD2,LOC151534,NGEF,
RAB17,SEPHS2,SLC9A3R1,SULT1A2,TMBIM6,TOM1,USH1C
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 SEPHS2


There's no related Drug.
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Cross referenced IDs for SEPHS2
* 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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