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 GLUD1

Basic gene info.	Gene symbol	GLUD1
	Gene name	glutamate dehydrogenase 1
	Synonyms	GDH\|GDH1\|GLUD
	Cytomap	UCSC genome browser: 10q23.3
	Genomic location	chr10 :88809958-88854776
	Type of gene	protein-coding
	RefGenes	NM_005271.3,
	Ensembl id	ENSG00000148672
	Description	GDH 1glutamate dehydrogenase (NAD(P)+)glutamate dehydrogenase 1, mitochondrial
	Modification date	20141219
dbXrefs	MIM : 138130
	HGNC : HGNC
	Ensembl : ENSG00000148672
	HPRD : 11748
	Vega : OTTHUMG00000018666
Protein	UniProt: P00367 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GLUD1
	BioGPS: 2746
	Gene Expression Atlas: ENSG00000148672
	The Human Protein Atlas: ENSG00000148672
Pathway	NCI Pathway Interaction Database: GLUD1
	KEGG: GLUD1
	REACTOME: GLUD1
	ConsensusPathDB
	Pathway Commons: GLUD1
Metabolism	MetaCyc: GLUD1
	HUMANCyc: GLUD1
Regulation	Ensembl's Regulation: ENSG00000148672
	miRBase: chr10 :88,809,958-88,854,776
	TargetScan: NM_005271
	cisRED: ENSG00000148672
Context	iHOP: GLUD1
	cancer metabolism search in PubMed: GLUD1
	UCL Cancer Institute: GLUD1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GLUD1 in cancer cell metabolism	1. Son J, Lyssiotis CA, Ying H, Wang X, Hua S, et al. (2013) Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496: 101-105. doi: 10.1038/nature12040. pmid: 3656466. go to article

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Phenotypic Information for GLUD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GLUD1
	Familial Cancer Database: GLUD1

* 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	138130; gene. 606762; phenotype.
Orphanet	35878; Hyperinsulinism-hyperammonemia syndrome.
Disease	KEGG Disease: GLUD1
	MedGen: GLUD1 (Human Medical Genetics with Condition)
	ClinVar: GLUD1
Phenotype	MGI: GLUD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GLUD1

Mutations for GLUD1

* 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	GLUD1	chr10	88831297	88831317	CNTN5	chr11	99433954	99433974
ovary	GLUD1	chr10	88831301	88831321	GLUD1	chr10	88844424	88844444
ovary	GLUD1	chr10	88831303	88831323	GLUD1	chr10	88844424	88844444
ovary	GLUD1	chr10	88832057	88832077	CNTN5	chr11	99427255	99427275

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 GLUD1 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
BM807517	GLUD1	19	186	10	88811238	88811405	HBG2	179	201	11	5350574	5350596
BI054523	UPF2	11	70	10	12071117	12071176	GLUD1	59	141	10	88811189	88811305

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=26)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr10:88827869-88827869	p.R231Q	2
chr10:88811597-88811597	p.L530V	2
chr10:88811617-88811617	p.R523H	2
chr10:88854313-88854313	p.G72R	1
chr10:88817490-88817490	p.T484T	1
chr10:88820487-88820487	p.E385E	1
chr10:88822583-88822583	p.A251T	1
chr10:88854320-88854320	p.M69I	1
chr10:88817495-88817495	p.G483*	1
chr10:88820502-88820502	p.I380I	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		5			3		2			2	4	1			4	7		6
# mutation	2	1		5			3		2			5	4	1			4	7		6
nonsynonymous SNV	2			3			2		2			3	3				1	4		3
synonymous SNV		1		2			1					2	1	1			3	3		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
chr10:88827869	p.R231Q	2
chr10:88854335	p.Y193C	1
chr10:88818945	p.D414H	1
chr10:88820771	p.I188S	1
chr10:88835729	p.I400I	1
chr10:88854340	p.A393T	1
chr10:88818952	p.L167L	1
chr10:88820788	p.I380I	1
chr10:88835744	p.V161I	1
chr10:88854398	p.T536I	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 GLUD1 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 GLUD1

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


ACADSB,ZFAND4,C10orf32,ESR1,FAM35A,FAM35DP,FAM35BP, FOXA1,GLUD1,GLUD2,HCAR1,MOAP1,NDFIP1,PLA2G12A, PTGR2,RAB5B,SLC39A9,TAPT1,TBC1D12,TTC8,XBP1	BZW1,CAB39L,DAZAP2,GLUD1,HIATL1,LOC653566,MEAF6, PIGK,RAB11A,REEP5,SEC22C,SELT,SEP15,SLC44A1, SNX14,TMCO1,TMEM59,SARAF,TMEM9B,UNC50,YWHAQ

ASCC1,ATAD1,ATP5C1,CALM2,COX15,CWF19L1,FAM35A, FAM35BP,GDI2,GHITM,GLRX3,GLUD1,GLUD2,GSTO1, MARCH5,MRPL43,NDUFB8,PCGF5,PPA1,SMNDC1,VPS26A	AKR1C3,BPHL,TMEM256,CRYL1,DERA,ELMOD2,FAM35A, FAM35BP,FAM3B,CMTR2,GLUD1,GLUD2,GRAMD1C,MAPK8, NCOA4,PHYH,PPP1CC,RRAS2,SAR1B,SUCLG1,TMEM139

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 GLUD1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28737; -.
Organism-specific databases	CTD	2746; -.

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
DB00142	glutamate dehydrogenase 1	approved; nutraceutical	L-Glutamic Acid
DB00157	glutamate dehydrogenase 1	approved; nutraceutical	NADH
DB00756	glutamate dehydrogenase 1	approved	Hexachlorophene
DB01907	glutamate dehydrogenase 1	experimental	Nicotinamide-Adenine-Dinucleotide
DB03431	glutamate dehydrogenase 1	experimental	Adenosine-5'-Diphosphate
DB04137	glutamate dehydrogenase 1	experimental	Guanosine-5'-Triphosphate
DB00130	glutamate dehydrogenase 1	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for GLUD1

* 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