Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	SMPD1
	Gene name	sphingomyelin phosphodiesterase 1, acid lysosomal
	Synonyms	ASM\|ASMASE\|NPD
	Cytomap	UCSC genome browser: 11p15.4-p15.1
	Genomic location	chr11 :6411643-6416228
	Type of gene	protein-coding
	RefGenes	NM_000543.4, NM_001007593.2,NR_027400.1,
	Ensembl id	ENSG00000166311
	Description	acid sphingomyelinasesphingomyelin phosphodiesterase
	Modification date	20141219
dbXrefs	MIM : 607608
	HGNC : HGNC
	Ensembl : ENSG00000166311
	HPRD : 06353
	Vega : OTTHUMG00000165453
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMPD1
	BioGPS: 6609
	Gene Expression Atlas: ENSG00000166311
	The Human Protein Atlas: ENSG00000166311
Pathway	NCI Pathway Interaction Database: SMPD1
	KEGG: SMPD1
	REACTOME: SMPD1
	ConsensusPathDB
	Pathway Commons: SMPD1
Metabolism	MetaCyc: SMPD1
	HUMANCyc: SMPD1
Regulation	Ensembl's Regulation: ENSG00000166311
	miRBase: chr11 :6,411,643-6,416,228
	TargetScan: NM_000543
	cisRED: ENSG00000166311
Context	iHOP: SMPD1
	cancer metabolism search in PubMed: SMPD1
	UCL Cancer Institute: SMPD1
Assigned class in ccmGDB	C

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Phenotypic Information for SMPD1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_SPHINGOLIPID_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SMPD1
	MedGen: SMPD1 (Human Medical Genetics with Condition)
	ClinVar: SMPD1
Phenotype	MGI: SMPD1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMPD1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AW951504	MAGEA4	1	144	X	151092694	151092837	SMPD1	141	493	11	6413115	6414884
BP375800	SMPD1	4	423	11	6411708	6412128	TRPC4	420	582	13	38357388	38443784
AA378043	MAGEA4	1	144	X	151092693	151092837	SMPD1	141	317	11	6413115	6413288
BF853689	SMPD1	54	256	11	6414495	6414926	SMPD1	252	456	11	6415198	6415558
AK057846	NIPA1	1	1914	15	23044062	23086291	SMPD1	1897	2065	11	6416059	6416227

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr11:6411935-6411935	p.V36A	4
chr11:6412931-6412931	p.D212D	2
chr11:6412745-6412745	p.R150R	2
chr11:6413332-6413332	p.A346V	2
chr11:6411931-6411942	p.V36_L39delVLAL	2
chr11:6413196-6413196	p.V301I	2
chr11:6414911-6414911	p.R399Q	2
chr11:6415463-6415463	p.G464R	1
chr11:6411960-6411960	p.A44A	1
chr11:6413100-6413100	p.A269P	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	4	1		9			1		1			3	4	1			3	7		10
# mutation	4	1		10			1		1			3	4	1			3	8		10
nonsynonymous SNV	4			8			1		1			2	4				2	6		7
synonymous SNV		1		2								1		1			1	2		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr11:6414487	p.R378H,SMPD1	2
chr11:6414911	p.R443Q,SMPD1	2
chr11:6413381	p.D212G,SMPD1	1
chr11:6412809	p.A346V,SMPD1	1
chr11:6415662	p.T588T,SMPD1	1
chr11:6413100	p.L216L,SMPD1	1
chr11:6414465	p.A357D,SMPD1	1
chr11:6412896	p.S600S,SMPD1	1
chr11:6415691	p.R230C,SMPD1	1
chr11:6413117	p.E358K,SMPD1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01151	sphingomyelin phosphodiesterase 1, acid lysosomal	approved	Desipramine
DB00143	sphingomyelin phosphodiesterase 1, acid lysosomal	approved; nutraceutical	Glutathione

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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