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 GLUL

Basic gene info.	Gene symbol	GLUL
	Gene name	glutamate-ammonia ligase
	Synonyms	GLNS\|GS\|PIG43\|PIG59
	Cytomap	UCSC genome browser: 1q31
	Genomic location	chr1 :182350838-182361341
	Type of gene	protein-coding
	RefGenes	NM_001033044.2, NM_001033056.2,NM_002065.5,
	Ensembl id	ENSG00000135821
	Description	cell proliferation-inducing protein 59glutamate decarboxylaseglutamate--ammonia ligaseglutamine synthaseglutamine synthetaseproliferation-inducing protein 43
	Modification date	20141207
dbXrefs	MIM : 138290
	HGNC : HGNC
	Ensembl : ENSG00000135821
	HPRD : 00701
	Vega : OTTHUMG00000037407
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GLUL
	BioGPS: 2752
	Gene Expression Atlas: ENSG00000135821
	The Human Protein Atlas: ENSG00000135821
Pathway	NCI Pathway Interaction Database: GLUL
	KEGG: GLUL
	REACTOME: GLUL
	ConsensusPathDB
	Pathway Commons: GLUL
Metabolism	MetaCyc: GLUL
	HUMANCyc: GLUL
Regulation	Ensembl's Regulation: ENSG00000135821
	miRBase: chr1 :182,350,838-182,361,341
	TargetScan: NM_001033044
	cisRED: ENSG00000135821
Context	iHOP: GLUL
	cancer metabolism search in PubMed: GLUL
	UCL Cancer Institute: GLUL
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GLUL
	Familial Cancer Database: GLUL

* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_NITROGEN_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for GLUL

* 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 GLUL 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
AW352004	GLUL	27	318	1	182355437	182357735	GLUL	308	393	1	182353773	182353858
CB322028	MTIF2	17	186	2	55463756	55463925	GLUL	182	636	1	182353606	182354693
DA275818	WDR74	1	102	11	62609180	62609281	GLUL	103	567	1	182353265	182353729
BF988852	GLUL	1	145	1	182353060	182353204	GLUL	137	244	1	182352944	182353051
BE765952	GLUL	2	78	1	182352479	182352556	SLC24A2	76	149	9	19509220	19509293
AV650942	SERP1	1	399	3	150299506	150301991	GLUL	389	598	1	182353126	182353336
AA581184	GLUL	1	62	1	182352164	182352225	GLUL	58	166	1	182352045	182352153
AW579277	PROS1	1	237	3	93678727	93678963	GLUL	231	294	1	182353484	182353547
BF932728	RUFY1	8	65	5	178993286	178993345	GLUL	58	237	1	182358989	182359169
BE765994	GLUL	1	75	1	182352482	182352556	SLC24A2	74	148	9	19509220	19509294
W27933	GLUL	40	214	1	182352976	182353150	GLUL	206	361	1	182357785	182360867
BF925573	GRAMD3	23	402	5	125827042	125827422	GLUL	388	481	1	182352164	182352256
AW168573	ART3	1	80	4	76942273	76942352	GLUL	74	134	1	182352031	182352091

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr1:182356408-182356408	p.F62F	2
chr1:182354926-182354926	p.A191V	2
chr1:182353655-182353655	p.Y336C	2
chr1:182356278-182356278	p.R106*	2
chr1:182356326-182356326	p.R90C	2
chr1:182353586-182353586	p.C359Y	1
chr1:182355421-182355421	p.W149R	1
chr1:182353707-182353707	p.R319C	1
chr1:182356407-182356407	p.D63N	1
chr1:182354584-182354584	p.T237T	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		7	1		1		1	1		5	4	1	1		3	6		7
# mutation		1		6	1		1		1	1		5	4	1	1		3	7		9
nonsynonymous SNV				4	1		1		1	1		2	4	1			2	6		5
synonymous SNV		1		2								3			1		1	1		4

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
chr1:182353767	p.A191V,GLUL	2
chr1:182354926	p.R299C,GLUL	2
chr1:182353654	p.Y336Y,GLUL	1
chr1:182356407	p.R222G,GLUL	1
chr1:182353797	p.D63N,GLUL	1
chr1:182354990	p.K333R,GLUL	1
chr1:182353664	p.A221T,GLUL	1
chr1:182356423	p.L57F,GLUL	1
chr1:182353819	p.Q331R,GLUL	1
chr1:182355001	p.P199S,GLUL	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 GLUL 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 GLUL

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


ABAT,C1orf27,KIAA0825,CD46,COG2,FAM63A,GLUL, HHAT,HNRNPH2,KIAA0040,LRG1,MAPT,MR1,NEK10, NEK11,RALGPS2,RCOR3,RUNDC1,SLC30A1,TOR1AIP1,XBP1	ACSM2A,ACSM2B,ALDH1L1,ASS1,IZUMO4,APMAP,CALCRL, CYP1A2,ECHDC3,GLUL,GLYCTK,HRSP12,MOCS1,MOGAT1, NTSR2,PC,PMM1,RASL10B,SHMT1,TCEB3,TMEM120A

ABCB4,ARNT,C1orf198,C1orf85,CYB5R1,GLP1R,GLUL, KIAA0087,LEFTY1,LOC92973,MR1,NCSTN,OR13J1,PBXIP1, PI4KB,RNASEL,RPLP0P2,SLAMF6,STX6,TMEM204,WDR26	APCDD1,BCAT1,CD3EAP,CP,EIF2AK4,FAM107A,FKBP5, GLUL,IRAK3,JPH1,LONRF1,LSM11,MRGPRX2,MUSK, PAPPA2,SCNN1G,SLC7A2,TBC1D8,VIT,VSIG8,ZBTB16

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 GLUL

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
DB02663	glutamate-ammonia ligase	experimental	2-Amino-4-(Hydroxymethyl-Phosphinyl)Butanoic Acid
DB03431	glutamate-ammonia ligase	experimental	Adenosine-5'-Diphosphate
DB00130	glutamate-ammonia ligase	approved; nutraceutical; investigational	L-Glutamine
DB00142	glutamate-ammonia ligase	approved; nutraceutical	L-Glutamic Acid

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Cross referenced IDs for GLUL

* 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