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 GNGT1

Basic gene info.	Gene symbol	GNGT1
	Gene name	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1
	Synonyms	GNG1
	Cytomap	UCSC genome browser: 7q21.3
	Genomic location	chr7 :93535819-93540485
	Type of gene	protein-coding
	RefGenes	NM_021955.3,
	Ensembl id	ENSG00000127928
	Description	guanine nucleotide-binding protein G(T) subunit gamma-T1transducin gamma chain
	Modification date	20141207
dbXrefs	MIM : 189970
	HGNC : HGNC
	Ensembl : ENSG00000127928
	HPRD : 01805
	Vega : OTTHUMG00000022908
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNGT1
	BioGPS: 2792
	Gene Expression Atlas: ENSG00000127928
	The Human Protein Atlas: ENSG00000127928
Pathway	NCI Pathway Interaction Database: GNGT1
	KEGG: GNGT1
	REACTOME: GNGT1
	ConsensusPathDB
	Pathway Commons: GNGT1
Metabolism	MetaCyc: GNGT1
	HUMANCyc: GNGT1
Regulation	Ensembl's Regulation: ENSG00000127928
	miRBase: chr7 :93,535,819-93,540,485
	TargetScan: NM_021955
	cisRED: ENSG00000127928
Context	iHOP: GNGT1
	cancer metabolism search in PubMed: GNGT1
	UCL Cancer Institute: GNGT1
Assigned class in ccmGDB	C

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Phenotypic Information for GNGT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNGT1
	Familial Cancer Database: GNGT1

* 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
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GNGT1
	MedGen: GNGT1 (Human Medical Genetics with Condition)
	ClinVar: GNGT1
Phenotype	MGI: GNGT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNGT1

Mutations for GNGT1

* 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 GNGT1 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
BF986197	GNGT1	17	204	7	93516054	93516607	GLG1	199	405	16	74514224	74519729
X93851	PSD3	1	80	8	18441287	18441366	GNGT1	76	230	7	93346824	93346977
AA303013	TMCO3	1	226	13	114204317	114204542	GNGT1	223	281	7	93516068	93516126
BI050757	PPP1R21	1	145	2	48725825	48734469	GNGT1	141	198	7	93518478	93518535
BM983864	PARD3B	2	21	2	205874391	205874410	GNGT1	18	398	7	93515859	93516603
AW995893	GNGT1	30	289	7	93516673	93518535	UBE2I	272	437	16	1375024	1375189

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=8)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr7:93536082-93536082	p.D8E	1
chr7:93540172-93540172	p.G56D	1
chr7:93536106-93536106	p.K16K	1
chr7:93540176-93540176	p.I57I	1
chr7:93536107-93536107	p.M17L	1
chr7:93540182-93540182	p.E59E	1
chr7:93536131-93536131	p.E25*	1
chr7:93540200-93540200	p.K65K	1
chr7:93536147-93536147	p.R30I	1
chr7:93540201-93540201	p.E66Q	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	1		1		1	1	1	1
# mutation				1								3	1		1		1	1	1	1
nonsynonymous SNV				1								3			1			1	1
synonymous SNV													1				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
chr7:93536082	p.M31K	1
chr7:93536150	p.V40I	1
chr7:93540123	p.G56D	1
chr7:93540172	p.E59E	1
chr7:93540182	p.K65K	1
chr7:93540200	p.E66Q	1
chr7:93540201	p.E66D	1
chr7:93540203	p.V3L	1
chr7:93536065	p.I4I	1
chr7:93536070	p.D8E	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 GNGT1 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 GNGT1

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


ADAMTS20,ALG1L,C12orf56,COA1,DEFB126,COL6A4P1,SPATA31D3, GJB7,GNGT1,GRK7,H2BFWT,HTR2C,KRTAP4-1,MCHR2, OR13H1,OR8D2,SLC25A2,SLC5A12,SPDYC,SPERT,TAS2R38	LINC01559,C7orf72,FAM151A,GNGT1,HNF1B,CEMIP,KRTAP4-1, LGSN,MAGEA4,NAPSA,NMU,OR13H1,OTOP2,SCEL, SCGB3A2,SERPINB3,SFTPB,TDRG1,TM4SF20,TR

C1orf111,RBM48,CALCR,CARD18,CGB2,GNGT1,INSM2, KRTAP27-1,LOC493754,LRCH4,NBPF6,PCLO,POLR2J4,RFPL2, RIMS2,RTP2,SBDSP1,SIM1,SLC12A9,TAS2R7,UNC5A	ABCG2,AMDHD2,KIAA1551,SH3D21,CACNA1D,COX6A2,CXADRP3, GLS,GNGT1,JMJD1C,KRT13,LOC154449,MGC27382,MIA2, OSGIN1,RSPH3,SLC16A5,SLC22A18,SLC26A1,TYW1B,UGT1A1

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 GNGT1

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
DB07752	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	experimental	FARNESYL
DB00945	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Acetylsalicylic acid
DB00394	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Beclomethasone
DB00443	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Betamethasone
DB01222	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Budesonide
DB01410	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Ciclesonide
DB01260	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Desonide
DB01234	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Dexamethasone
DB00180	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Flunisolide
DB00588	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; investigational	Fluticasone Propionate
DB00741	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Hydrocortisone
DB00959	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Methylprednisolone
DB00764	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Mometasone
DB01384	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Paramethasone
DB00860	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Prednisolone
DB00635	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Prednisone
DB00896	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Rimexolone
DB00620	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Triamcinolone
DB00125	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; nutraceutical	L-Arginine
DB00155	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; nutraceutical	L-Citrulline
DB00435	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Nitric Oxide
DB00988	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Dopamine
DB00171	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; nutraceutical	Adenosine triphosphate
DB00131	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved; nutraceutical	Adenosine monophosphate
DB00396	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	approved	Progesterone

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Cross referenced IDs for GNGT1

* 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