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 SMPD1
Basic gene info.Gene symbolSMPD1
Gene namesphingomyelin phosphodiesterase 1, acid lysosomal
SynonymsASM|ASMASE|NPD
CytomapUCSC genome browser: 11p15.4-p15.1
Genomic locationchr11 :6411643-6416228
Type of geneprotein-coding
RefGenesNM_000543.4,
NM_001007593.2,NR_027400.1,
Ensembl idENSG00000166311
Descriptionacid sphingomyelinasesphingomyelin phosphodiesterase
Modification date20141219
dbXrefs MIM : 607608
HGNC : HGNC
Ensembl : ENSG00000166311
HPRD : 06353
Vega : OTTHUMG00000165453
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMPD1
BioGPS: 6609
Gene Expression Atlas: ENSG00000166311
The Human Protein Atlas: ENSG00000166311
PathwayNCI Pathway Interaction Database: SMPD1
KEGG: SMPD1
REACTOME: SMPD1
ConsensusPathDB
Pathway Commons: SMPD1
MetabolismMetaCyc: SMPD1
HUMANCyc: SMPD1
RegulationEnsembl's Regulation: ENSG00000166311
miRBase: chr11 :6,411,643-6,416,228
TargetScan: NM_000543
cisRED: ENSG00000166311
ContextiHOP: SMPD1
cancer metabolism search in PubMed: SMPD1
UCL Cancer Institute: SMPD1
Assigned class in ccmGDBC

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Phenotypic Information for SMPD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMPD1
Familial Cancer Database: SMPD1
* 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: SMPD1
MedGen: SMPD1 (Human Medical Genetics with Condition)
ClinVar: SMPD1
PhenotypeMGI: SMPD1 (International Mouse Phenotyping Consortium)
PhenomicDB: SMPD1

Mutations for SMPD1
* 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 SMPD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW951504MAGEA41144X151092694151092837SMPD11414931164131156414884
BP375800SMPD144231164117086412128TRPC4420582133835738838443784
AA378043MAGEA41144X151092693151092837SMPD11413171164131156413288
BF853689SMPD1542561164144956414926SMPD12524561164151986415558
AK057846NIPA111914152304406223086291SMPD1189720651164160596416227

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=43)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=2)

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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
chr11:6411935-6411935p.V36A4
chr11:6411931-6411942p.V36_L39delVLAL2
chr11:6413196-6413196p.V301I2
chr11:6414911-6414911p.R399Q2
chr11:6412931-6412931p.D212D2
chr11:6412745-6412745p.R150R2
chr11:6413332-6413332p.A346V2
chr11:6411930-6411942p.L35fs*381
chr11:6413002-6413002p.P236L1
chr11:6415560-6415560p.R496M1

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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
# sample41 9  1 1  341  37 10
# mutation41 10  1 1  341  38 10
nonsynonymous SNV4  8  1 1  24   26 7
synonymous SNV 1 2       1 1  12 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
chr11:6414487p.R378H,SMPD12
chr11:6414911p.R443Q,SMPD12
chr11:6412017p.P63P,SMPD11
chr11:6415153p.L259V,SMPD11
chr11:6412983p.F456F,SMPD11
chr11:6415745p.V77L,SMPD11
chr11:6413196p.L263F,SMPD11
chr11:6412057p.E471K,SMPD11
chr11:6415196p.P92S,SMPD11
chr11:6412984p.A269P,SMPD11

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 SMPD1 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 SMPD1

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

CERCAM,CHID1,CHPF,CLEC11A,COPZ2,FAM20C,GPC1,
IFI27L2,ILK,LEPRE1,LRPAP1,MRC2,MXRA8,NAGLU,
RNH1,SDF4,SLC39A13,SMPD1,TGFB1,TSPAN4,VENTX
ACP2,ACTR1A,AP2S1,ATP6V0D1,BLVRB,LAMTOR1,CCM2,
DHRS7B,NDUFAF3,OAZ1,PSEN2,PSMB6,PSMC4,RNH1,
RNPEPL1,LAMTOR2,SEC13,SERF2,SLC2A8,SMPD1,UROD

C11orf86,LINC00520,C1orf94,CAPN11,CDHR2,CIDEC,CLCA4,
CLDN23,DHRS9,GLRA4,GUCA2A,GUCA2B,FAM214B,MYPN,
OR2G3,RSAD2,SMPD1,TRANK1,UGT1A4,UGT1A5,VSIG1
ARHGEF18,BSG,CAB39,CEACAM5,CGN,CTNNA1,FBLIM1,
GBA,GBAP1,GNA13,GPRC5A,KIF16B,LRP10,PEX26,
PLAC8,RHOF,SMPD1,SPATS2L,STX3,TBC1D2,TMEM127
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 SMPD1
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
DB01151sphingomyelin phosphodiesterase 1, acid lysosomalapprovedDesipramine
DB00143sphingomyelin phosphodiesterase 1, acid lysosomalapproved; nutraceuticalGlutathione


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Cross referenced IDs for SMPD1
* 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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