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 SMPD4

Basic gene info.	Gene symbol	SMPD4
	Gene name	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)
	Synonyms	NET13\|NSMASE-3\|NSMASE3
	Cytomap	UCSC genome browser: 2q21.1
	Genomic location	chr2 :130908964-130939330
	Type of gene	protein-coding
	RefGenes	NM_001171084.1, NM_001171083.2,NM_017751.4,NM_017951.4,NR_033230.2, NR_033231.2,NR_033232.2,
	Ensembl id	ENSG00000136699
	Description	SKNY proteinneutral sphingomyelinase 3neutral sphingomyelinase IIIsphingomyelin phosphodiesterase 4
	Modification date	20141207
dbXrefs	MIM : 610457
	HGNC : HGNC
	Ensembl : ENSG00000136699
	HPRD : 13374
	Vega : OTTHUMG00000131624
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMPD4
	BioGPS: 55627
	Gene Expression Atlas: ENSG00000136699
	The Human Protein Atlas: ENSG00000136699
Pathway	NCI Pathway Interaction Database: SMPD4
	KEGG: SMPD4
	REACTOME: SMPD4
	ConsensusPathDB
	Pathway Commons: SMPD4
Metabolism	MetaCyc: SMPD4
	HUMANCyc: SMPD4
Regulation	Ensembl's Regulation: ENSG00000136699
	miRBase: chr2 :130,908,964-130,939,330
	TargetScan: NM_001171084
	cisRED: ENSG00000136699
Context	iHOP: SMPD4
	cancer metabolism search in PubMed: SMPD4
	UCL Cancer Institute: SMPD4
Assigned class in ccmGDB	C

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Phenotypic Information for SMPD4(metabolism pathway, cancer, disease, phenome)

Cancer 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/

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: SMPD4
	MedGen: SMPD4 (Human Medical Genetics with Condition)
	ClinVar: SMPD4
Phenotype	MGI: SMPD4 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 SMPD4 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
AK126162	SMPD4	1	1559	2	130919680	130921238	MTCH1	1557	2115	6	36935918	36936476
AA315813	SMPD4	1	220	2	130932487	130939151	MDH1	219	495	2	63821620	63824707
AW951984	SMPD4	1	219	2	130932487	130939150	MDH1	218	333	2	63821620	63824547

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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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=3

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Somatic 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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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
chr2:130910990-130910990	p.A682P	3
chr2:130930247-130930247	p.P192L	3
chr2:130910962-130910962	p.G691E	3
chr2:130912789-130912789	p.F484V	2
chr2:130910182-130910182	p.L849L	2
chr2:130934161-130934161	p.A41V	2
chr2:130914230-130914230	p.F411L	2
chr2:130912778-130912778	p.F487F	2
chr2:130931109-130931109	p.V122M	1
chr2:130910174-130910174	p.S852F	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=3

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	3	1		8			3			2		10	8				10	9	1	9
# mutation	3	1		8			3			2		10	8				10	10	1	10
nonsynonymous SNV	2			6			3			2		7	8				6	7	1	8
synonymous SNV	1	1		2								3					4	3		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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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
chr2:130930247	p.P119L,SMPD4	3
chr2:130931133	p.V114M,SMPD4	2
chr2:130910919	p.L747L,SMPD4	1
chr2:130918787	p.E571K,SMPD4	1
chr2:130911453	p.L390F,SMPD4	1
chr2:130930378	p.G177R,SMPD4	1
chr2:130910182	p.I22S,SMPD4	1
chr2:130912765	p.G733G,SMPD4	1
chr2:130939110	p.L563L,SMPD4	1
chr2:130910937	p.E373D,SMPD4	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 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

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


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

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 SMPD4

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
DB00144	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	approved; nutraceutical	Phosphatidylserine

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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