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 MBOAT1

Basic gene info.	Gene symbol	MBOAT1
	Gene name	membrane bound O-acyltransferase domain containing 1
	Synonyms	1\|LPEAT1\|LPLAT\|LPLAT 1\|LPSAT\|OACT1\|dJ434O11.1
	Cytomap	UCSC genome browser: 6p22.3
	Genomic location	chr6 :20100934-20212670
	Type of gene	protein-coding
	RefGenes	NM_001080480.2, NR_073465.1,
	Ensembl id	ENSG00000172197
	Description	1-acylglycerophosphoserine O-acyltransferaseO-acyltransferase (membrane bound) domain containing 1O-acyltransferase domain-containing protein 1lyso-PS acyltransferaselysophosphatidylethanolamine acyltransferase 1lysophosphatidylserine acyltransferase
	Modification date	20141207
dbXrefs	MIM : 611732
	HGNC : HGNC
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MBOAT1
	BioGPS: 154141
	Gene Expression Atlas: ENSG00000172197
	The Human Protein Atlas: ENSG00000172197
Pathway	NCI Pathway Interaction Database: MBOAT1
	KEGG: MBOAT1
	REACTOME: MBOAT1
	ConsensusPathDB
	Pathway Commons: MBOAT1
Metabolism	MetaCyc: MBOAT1
	HUMANCyc: MBOAT1
Regulation	Ensembl's Regulation: ENSG00000172197
	miRBase: chr6 :20,100,934-20,212,670
	TargetScan: NM_001080480
	cisRED: ENSG00000172197
Context	iHOP: MBOAT1
	cancer metabolism search in PubMed: MBOAT1
	UCL Cancer Institute: MBOAT1
Assigned class in ccmGDB	C

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Phenotypic Information for MBOAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MBOAT1
	Familial Cancer Database: MBOAT1

* 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_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MBOAT1
	MedGen: MBOAT1 (Human Medical Genetics with Condition)
	ClinVar: MBOAT1
Phenotype	MGI: MBOAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MBOAT1

Mutations for MBOAT1

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	MBOAT1	chr6	20111928	20112128	TNC	chr9	117857870	117858070
ovary	MBOAT1	chr6	20111948	20112148	TNC	chr9	117857868	117858068
ovary	MBOAT1	chr6	20162246	20162266		chr6	28918212	28918232
pancreas	MBOAT1	chr6	20111972	20112172	TNC	chr9	117857825	117858025
pancreas	MBOAT1	chr6	20112026	20112226	TNC	chr9	117857662	117857862

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MBOAT1 related fusion information.

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

AJ705329

MBOAT1

186

20124933

20125119

RPL37

180

374

40832556

40834357

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr6:20128943-20128943	p.R173*	2
chr6:20152869-20152869	p.I77I	2
chr6:20124775-20124775	p.T257T	2
chr6:20118754-20118754	p.A309T	2
chr6:20113188-20113188	p.L376L	2
chr6:20109870-20109870	p.F441fs*2	1
chr6:20126922-20126922	p.P180P	1
chr6:20113210-20113210	p.P369H	1
chr6:20152858-20152858	p.G81D	1
chr6:20124704-20124704	p.R281Q	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	1	3		9	1		3		2			4		1			1	7		9
# mutation	1	3		8	1		3		2			4		1			1	7		11
nonsynonymous SNV		1		7	1		2					3		1				5		5
synonymous SNV	1	2		1			1		2			1					1	2		6

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
chr6:20124704	p.A309T	2
chr6:20113188	p.R281Q	2
chr6:20124775	p.T257T	2
chr6:20118754	p.L376L	2
chr6:20113107	p.I123T	1
chr6:20212446	p.P369H	1
chr6:20144532	p.V113A	1
chr6:20113163	p.R364Q	1
chr6:20124709	p.M93I	1
chr6:20151460	p.K335R	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 MBOAT1 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 MBOAT1

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


ATP6V1B1,C5orf42,CDK19,CTNND2,DRD1,ELOVL2,FAM8A1, HOOK1,KDM1B,MAGI1,MBOAT1,NIPAL3,NUP153,OR4F15, PTPN13,RALBP1,RB1CC1,SYNJ2,TAC3,UBR5,VEZF1	AAGAB,AGR3,C3orf52,CA12,CDH1,CDS1,FBXO16, GOLM1,HHAT,MARVELD2,MBOAT1,PIP4K2C,PPAPDC1B,PRRG4, RUNDC1,SEC14L2,TPD52,TTC39A,TTC8,XBP1,ZYG11A

TMEM246,CREB3L1,ERN2,GALNT12,GFI1,GRIN1,HMG20B, KCNK1,KLF4,MBOAT1,MLPH,MRAP2,SERINC4,SGSM3, SIDT1,SLC22A23,ST6GALNAC1,SYTL1,TSPAN13,VWA3B,ZBTB7C	ACSS2,AGFG2,ATP8B1,C5orf30,CCDC88C,CD24,HARS2, MARVELD2,MBOAT1,MKRN1,NSF,PIGR,PRR5L,SDHA, SH3BGRL2,SH3BP1,SH3KBP1,SLC4A4,TNK1,TRAF3IP2,ZNF217

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 MBOAT1

There's no related Drug.

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Cross referenced IDs for MBOAT1

* 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