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 SMPD4
Basic gene info.Gene symbolSMPD4
Gene namesphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)
SynonymsNET13|NSMASE-3|NSMASE3
CytomapUCSC genome browser: 2q21.1
Genomic locationchr2 :130908964-130939330
Type of geneprotein-coding
RefGenesNM_001171084.1,
NM_001171083.2,NM_017751.4,NM_017951.4,NR_033230.2,
NR_033231.2,NR_033232.2,
Ensembl idENSG00000136699
DescriptionSKNY proteinneutral sphingomyelinase 3neutral sphingomyelinase IIIsphingomyelin phosphodiesterase 4
Modification date20141207
dbXrefs MIM : 610457
HGNC : HGNC
Ensembl : ENSG00000136699
HPRD : 13374
Vega : OTTHUMG00000131624
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMPD4
BioGPS: 55627
Gene Expression Atlas: ENSG00000136699
The Human Protein Atlas: ENSG00000136699
PathwayNCI Pathway Interaction Database: SMPD4
KEGG: SMPD4
REACTOME: SMPD4
ConsensusPathDB
Pathway Commons: SMPD4
MetabolismMetaCyc: SMPD4
HUMANCyc: SMPD4
RegulationEnsembl's Regulation: ENSG00000136699
miRBase: chr2 :130,908,964-130,939,330
TargetScan: NM_001171084
cisRED: ENSG00000136699
ContextiHOP: SMPD4
cancer metabolism search in PubMed: SMPD4
UCL Cancer Institute: SMPD4
Assigned class in ccmGDBC

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Phenotypic Information for SMPD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMPD4
Familial Cancer Database: SMPD4
* 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_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SMPD4
MedGen: SMPD4 (Human Medical Genetics with Condition)
ClinVar: SMPD4
PhenotypeMGI: SMPD4 (International Mouse Phenotyping Consortium)
PhenomicDB: SMPD4

Mutations for SMPD4
* 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 SMPD4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK126162SMPD4115592130919680130921238MTCH11557211563693591836936476
AA315813SMPD412202130932487130939151MDH121949526382162063824707
AW951984SMPD412192130932487130939150MDH121833326382162063824547

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          1      
GAIN (# sample)                 
LOSS (# sample)          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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
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
chr2:130930247-130930247p.P192L3
chr2:130910962-130910962p.G691E3
chr2:130910990-130910990p.A682P3
chr2:130934161-130934161p.A41V2
chr2:130914230-130914230p.F411L2
chr2:130912778-130912778p.F487F2
chr2:130912789-130912789p.F484V2
chr2:130910182-130910182p.L849L2
chr2:130930227-130930227p.F199L1
chr2:130910728-130910728p.R720Q1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 8  3  2 108   10919
# mutation31 8  3  2 108   1010110
nonsynonymous SNV2  6  3  2 78   6718
synonymous SNV11 2       3    43 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
chr2:130930247p.P119L,SMPD43
chr2:130931133p.V114M,SMPD42
chr2:130910182p.G733G,SMPD41
chr2:130912765p.L563L,SMPD41
chr2:130939110p.E373D,SMPD41
chr2:130910937p.W160C,SMPD41
chr2:130918802p.L708M,SMPD41
chr2:130911458p.E561K,SMPD41
chr2:130930381p.P344L,SMPD41
chr2:130910224p.L158M,SMPD41

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 SMPD4 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 SMPD4

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

ATG4B,CHTF18,COPS7B,DAZAP1,DDX12P,DHX34,ERCC3,
FBRSL1,ILF3,IMP4,IWS1,LOC150776,LOC642846,POLR2D,
RAVER1,SAP130,SMPD4,SRRT,STK25,TMEM177,WDR33
ASB6,ATF6B,LRRC75B,CHERP,CNOT3,DHX34,ELMO3,
DENND6B,FBXW9,KIF22,LIG1,RAD9A,SCAMP4,SLC12A9,
SLC25A29,SMPD4,STK11IP,TRIM28,USP20,WDR6,ZFYVE27

ATG4B,SPATA33,CAPN10,CENPO,CHTF18,DBF4B,DHX34,
E2F1,ILF3,ING5,KIF18B,LOC150776,MYBL2,POLR1A,
POLR2D,RECQL4,SMPD4,SMYD5,STK25,WDR33,ZNF142
ATRIP,CEP164,DHX30,DOHH,EIF3B,GCN1L1,HNRNPA0,
ILF3,KHSRP,MYBBP1A,NOC2L,NOL6,NUP188,ODF2,
PFAS,SLC7A1,SMPD4,TELO2,TMEM201,ZC3H18,ZNF142
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 SMPD4
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
DB00144sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)approved; nutraceuticalPhosphatidylserine


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Cross referenced IDs for SMPD4
* 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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