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 GAD1

Basic gene info.	Gene symbol	GAD1
	Gene name	glutamate decarboxylase 1 (brain, 67kDa)
	Synonyms	CPSQ1\|GAD\|SCP
	Cytomap	UCSC genome browser: 2q31
	Genomic location	chr2 :171673199-171699269
	Type of gene	protein-coding
	RefGenes	NM_000817.2, NM_013445.3,
	Ensembl id	ENSG00000128683
	Description	67 kDa glutamic acid decarboxylaseGAD-67glutamate decarboxylase 1glutamate decarboxylase 67 kDa isoform
	Modification date	20141222
dbXrefs	MIM : 605363
	HGNC : HGNC
	Ensembl : ENSG00000128683
	HPRD : 12011
	Vega : OTTHUMG00000044175
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GAD1
	BioGPS: 2571
	Gene Expression Atlas: ENSG00000128683
	The Human Protein Atlas: ENSG00000128683
Pathway	NCI Pathway Interaction Database: GAD1
	KEGG: GAD1
	REACTOME: GAD1
	ConsensusPathDB
	Pathway Commons: GAD1
Metabolism	MetaCyc: GAD1
	HUMANCyc: GAD1
Regulation	Ensembl's Regulation: ENSG00000128683
	miRBase: chr2 :171,673,199-171,699,269
	TargetScan: NM_000817
	cisRED: ENSG00000128683
Context	iHOP: GAD1
	cancer metabolism search in PubMed: GAD1
	UCL Cancer Institute: GAD1
Assigned class in ccmGDB	C

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Phenotypic Information for GAD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GAD1
	Familial Cancer Database: GAD1

* 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_BETA_ALANINE_METABOLISM KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM KEGG_BUTANOATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GAD1
	MedGen: GAD1 (Human Medical Genetics with Condition)
	ClinVar: GAD1
Phenotype	MGI: GAD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GAD1

Mutations for GAD1

* 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 GAD1 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
AW162120	SGSM2	8	148	17	2284208	2284348	GAD1	144	670	2	171705814	171716272
DA078791	GAD1	1	274	2	171673400	171675153	ALDOC	274	581	17	26901972	26902481
AW609892	GAD1	4	24	2	171690266	171690286	PARD3	22	470	10	34606035	34620262
M85674	GAD1	1	268	2	171715328	171716410	RUNX1T1	268	382	8	93030731	93030844

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=59)	Stat. for Synonymous SNVs (# total SNVs=13)

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
chr2:171686107-171686107	p.R90C	4
chr2:171687555-171687555	p.R134C	3
chr2:171693312-171693312	p.R186L	3
chr2:171678659-171678659	p.G49S	2
chr2:171687621-171687621	p.L156L	2
chr2:171686061-171686061	p.K74N	2
chr2:171678609-171678609	p.W32*	2
chr2:171705817-171705817	p.L381F	2
chr2:171702536-171702536	p.A322D	2
chr2:171705836-171705836	p.R387H	2

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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=4

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	4	2		14	1		1	1	1	1		8	5	1			14	10		8
# mutation	4	2		15	1		1	1	1	1		9	6	1			16	10		9
nonsynonymous SNV	4	2		13	1		1		1			7	5	1			12	6		6
synonymous SNV				2				1		1		2	1				4	4		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
chr2:171702556	p.K74N,GAD1	3
chr2:171686061	p.L329I	3
chr2:171686107	p.A219A	2
chr2:171702021	p.R134C,GAD1	2
chr2:171716238	p.A544G	2
chr2:171687555	p.A253T	2
chr2:171700573	p.R90C,GAD1	2
chr2:171686090	p.D122Y,GAD1	1
chr2:171702114	p.K334N	1
chr2:171716383	p.G506G	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 GAD1 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 GAD1

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


ANKRD20A4,ANKRD20A8P,FAM215A,DENND1B,EVL,FMO5,GAD1, IQCF1,FAM214A,LOC440925,LOC728606,LRRC6,MAP2K4,MYO3B, NEK10,PKIB,SCGB1D2,SP5,TNK1,TPRG1,ULK4	LINC00314,CDH7,ELAVL2,GAD1,GUCY1B2,HAO2,IGFL1, KCNU1,KRT26,MAGEC2,MYO3A,MYO3B,RLN2,ROBO2, SLC22A1,SNORA4,SOX14,STXBP5L,SYT1,TEX14,ZPLD1

AGR2,ALOXE3,MYRF,CABLES1,CASP4,CCK,DPP4, ETV5,FOXD1,GAD1,KCNJ3,MTCL1,LHB,LMF2, LOC440925,LRRC16A,SOX13,SP5,TCIRG1,TRNP1,ZFPM1	CYP4F30P,CEACAM3,DEFA1B,RIPPLY3,EPB41L4A,GAD1,GJB4, GNRHR,GPR12,HPVC1,KRTAP13-2,MORF4,MSMB,OR2S2, OTX1,PAPPA2,TAPT1,TMEM105,SYNDIG1L,UNC5C,ZNF720

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 GAD1

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
DB00114	glutamate decarboxylase 1 (brain, 67kDa)	nutraceutical	Pyridoxal Phosphate
DB00142	glutamate decarboxylase 1 (brain, 67kDa)	approved; nutraceutical	L-Glutamic Acid

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Cross referenced IDs for GAD1

* 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