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 SMOX
Basic gene info.Gene symbolSMOX
Gene namespermine oxidase
SynonymsC20orf16|PAO|PAO-1|PAO1|PAOH|PAOH1|SMO
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :4129449-4168369
Type of geneprotein-coding
RefGenesNM_001270691.1,
NM_175839.2,NM_175840.2,NM_175841.2,NM_175842.2,
Ensembl idENSG00000088826
Descriptionflavin containing amine oxidaseflavin-containing spermine oxidasepolyamine oxidase 1putative cyclin G1 interacting protein
Modification date20141207
dbXrefs MIM : 615854
HGNC : HGNC
Ensembl : ENSG00000088826
HPRD : 11587
Vega : OTTHUMG00000031777
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMOX
BioGPS: 54498
Gene Expression Atlas: ENSG00000088826
The Human Protein Atlas: ENSG00000088826
PathwayNCI Pathway Interaction Database: SMOX
KEGG: SMOX
REACTOME: SMOX
ConsensusPathDB
Pathway Commons: SMOX
MetabolismMetaCyc: SMOX
HUMANCyc: SMOX
RegulationEnsembl's Regulation: ENSG00000088826
miRBase: chr20 :4,129,449-4,168,369
TargetScan: NM_001270691
cisRED: ENSG00000088826
ContextiHOP: SMOX
cancer metabolism search in PubMed: SMOX
UCL Cancer Institute: SMOX
Assigned class in ccmGDBC

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

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

Mutations for SMOX
* 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 SMOX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF769727SMOX15932041679164167994SMOX902532041634694164277
BC019054SMOX4915092041581514168367URM1151028399131133640131153013

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 # sample      2 2        
GAIN (# sample)      1          
LOSS (# sample)      1 2        
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=52)
Stat. for Synonymous SNVs
(# total SNVs=19)
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
chr20:4163144-4163144p.Q340*3
chr20:4164168-4164168p.R466Q2
chr20:4162483-4162483p.D157N2
chr20:4162485-4162485p.D157D2
chr20:4168011-4168011p.R542H2
chr20:4158083-4158083p.L98L2
chr20:4163401-4163401p.S425S2
chr20:4163028-4163028p.R301Q2
chr20:4162600-4162600p.A196S2
chr20:4155796-4155796p.A32T2

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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
# sample311101   3  64   75 17
# mutation31191   3  64   75 20
nonsynonymous SNV3  41   2  44   45 17
synonymous SNV 115    1  2    3  3
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
chr20:4162483p.D157N,SMOX3
chr20:4163401p.R179H,SMOX2
chr20:4162550p.R466Q,SMOX2
chr20:4164168p.S425S,SMOX2
chr20:4163035p.R177L,SMOX1
chr20:4168031p.S312P,SMOX1
chr20:4155822p.L452L,SMOX1
chr20:4163291p.R179C,SMOX1
chr20:4162601p.S312S,SMOX1
chr20:4164184p.P459H,SMOX1

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 SMOX 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 SMOX

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

BCL11A,SMCO4,CEBPB,DPYS,DUOXA2,UBALD2,FCN3,
ITIH4,KCNG2,KIFC3,MT1F,MT1L,MT1X,MT2A,
NRTN,POLR2F,SLC7A5,SMOX,TGFA,TRMU,TSPO
AHCY,AP1M2,ARRDC1,ASTN2,ATP13A1,BATF,HID1,
EMC10,DAK,ECE2,FAM83F,CAMSAP3,MARCKSL1,NIPSNAP1,
PICK1,PYCR1,SMOX,SMPDL3B,ST14,STAP2,TRPM4

ANKEF1,AP5S1,CDS2,CENPB,CSNK2A1,DDRGK1,FAM110A,
NSFL1C,PANK2,PSMF1,PTPRA,RBCK1,RRBP1,SMOX,
STK35,TASP1,TBC1D20,TRMT6,UBOX5,VPS16,ZCCHC3
CDH5,COL18A1,DOC2B,ENG,GREB1,HSPA12B,CEMIP,
KRT7,LRRC37A3,MFRP,MMP2,MMRN2,PCDHGA12,PECAM1,
PLXND1,POLR3H,RGS12,SMOX,SRPX2,TIE1,ZAR1L
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 SMOX
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00127spermine oxidaseapproved; nutraceuticalSpermine


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Cross referenced IDs for SMOX
* 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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