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 MGLL

Basic gene info.	Gene symbol	MGLL
	Gene name	monoglyceride lipase
	Synonyms	HU-K5\|HUK5\|MAGL\|MGL
	Cytomap	UCSC genome browser: 3q21.3
	Genomic location	chr3 :127407904-127542093
	Type of gene	protein-coding
	RefGenes	NM_001003794.2, NM_001256585.1,NM_007283.6,
	Ensembl id	ENSG00000074416
	Description	lysophospholipase homologmonoacylglycerol lipase
	Modification date	20141207
dbXrefs	MIM : 609699
	HGNC : HGNC
	Ensembl : ENSG00000074416
	HPRD : 17574
	Vega : OTTHUMG00000159641
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGLL
	BioGPS: 11343
	Gene Expression Atlas: ENSG00000074416
	The Human Protein Atlas: ENSG00000074416
Pathway	NCI Pathway Interaction Database: MGLL
	KEGG: MGLL
	REACTOME: MGLL
	ConsensusPathDB
	Pathway Commons: MGLL
Metabolism	MetaCyc: MGLL
	HUMANCyc: MGLL
Regulation	Ensembl's Regulation: ENSG00000074416
	miRBase: chr3 :127,407,904-127,542,093
	TargetScan: NM_001003794
	cisRED: ENSG00000074416
Context	iHOP: MGLL
	cancer metabolism search in PubMed: MGLL
	UCL Cancer Institute: MGLL
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MGLL in cancer cell metabolism	1. Galli GG, Multhaupt HA, Carrara M, de Lichtenberg KH, Christensen IB, et al. (2014) Prdm5 suppresses Apc(Min)-driven intestinal adenomas and regulates monoacylglycerol lipase expression. Oncogene 33: 3342-3350. doi: 10.1038/onc.2013.283. go to article 2. Cadenas C, Vosbeck S, Hein EM, Hellwig B, Langer A, et al. (2012) Glycerophospholipid profile in oncogene-induced senescence. Biochim Biophys Acta 1821: 1256-1268. doi: 10.1016/j.bbalip.2011.11.008. go to article

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

Cancer Description
Cancer	CGAP: MGLL
	Familial Cancer Database: MGLL

* 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 REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for MGLL

* 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	MGLL	chr3	127438066	127438086		chr3	127564415	127564435
ovary	MGLL	chr3	127522999	127523019	MGLL	chr3	127525693	127525713
ovary	MGLL	chr3	127528070	127528090	PCGF6	chr10	105086403	105086423
ovary	MGLL	chr3	127528122	127528142		chr10	120727510	120727530
ovary	MGLL	chr3	127530155	127530175	NR2E1	chr6	108489988	108490008
pancreas	MGLL	chr3	127461420	127461440		chr3	127406005	127406025

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 MGLL 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
BF819641	FLNA	10	365	X	153580934	153581464	MGLL	359	615	3	127411024	127413933
AI817662	MGLL	2	125	3	127410960	127411083	MGLL	120	359	3	127408820	127409210
BI014363	MGLL	1	100	3	127509273	127509373	HDLBP	101	186	2	242169019	242169104

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=10)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr3:127540605-127540605	p.L19L	2
chr3:127439932-127439932	p.L148L	2
chr3:127439934-127439934	p.L148L	2
chr3:127413955-127413955	p.V217I	1
chr3:127439949-127439949	p.V143I	1
chr3:127540540-127540540	p.P41H	1
chr3:127413976-127413976	p.G210S	1
chr3:127439970-127439970	p.P136S	1
chr3:127414007-127414007	p.L199L	1
chr3:127439973-127439977	p.E134fs*19	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		1	4							1	2	1				6	1		3
# mutation	1		1	4							1	2	1				7	1		3
nonsynonymous SNV	1			2								1	1				5			2
synonymous SNV			1	2							1	1					2	1		1

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
chr3:127439934	p.L148L,MGLL	2
chr3:127414007	p.A164V,MGLL	1
chr3:127500709	p.E154Q,MGLL	1
chr3:127414013	p.P136S,MGLL	1
chr3:127500727	p.V95I,MGLL	1
chr3:127429437	p.S83S,MGLL	1
chr3:127540634	p.P283S,MGLL	1
chr3:127429497	p.G81E,MGLL	1
chr3:127540652	p.S261F,MGLL	1
chr3:127429498	p.G52E,MGLL	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 MGLL 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 MGLL

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


ACACB,AOC3,AQP7,AQP7P1,ARHGEF15,C14orf180,CD300LG, CIDEC,GLYAT,GPD1,GPR146,KCNIP2,LIPE,MGLL, NPR1,PDE2A,PLIN1,PLIN4,RDH5,ROBO4,VWF	AIFM2,AOC3,CALB2,DMGDH,EHD2,EPHX1,GPD1, HEPN1,CTIF,KLB,LIPE,MCAM,MGLL,MRAS, MYO1C,NPR1,PLIN1,RBP4,RETSAT,SLC29A4,TUSC5

ATP2A3,B3GALT4,BCAS1,CAPN5,CCNG2,CDHR5,FER1L6, GSN,FAM214B,LIPH,LOC646627,MGLL,MMP28,MUC2, PLA2G10,PRKCD,SCNN1A,ST3GAL4,ST6GALNAC6,TSPAN1,VSIG2	ACOX1,APPL2,BAHD1,STPG1,CA4,CAPN2,CGN, RHOV___CHP1,CLCN2,CNNM4,CTSA,ENPP1,GBA,MAST2, MGLL,PEX26,RNF103,RUNDC1,SFXN1,SGK2,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 MGLL

There's no related Drug.

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Cross referenced IDs for MGLL

* 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