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 GNG2
Basic gene info.Gene symbolGNG2
Gene nameguanine nucleotide binding protein (G protein), gamma 2
Synonyms-
CytomapUCSC genome browser: 14q21
Genomic locationchr14 :52327021-52436518
Type of geneprotein-coding
RefGenesNM_001243773.1,
NM_001243774.1,NM_053064.4,
Ensembl idENSG00000186469
Descriptiong gamma-Iguanine nucleotide binding protein gamma 2guanine nucleotide-binding protein G(I)/G(O) gamma-2 subunitguanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Modification date20141207
dbXrefs MIM : 606981
HGNC : HGNC
Ensembl : ENSG00000186469
HPRD : 16234
Vega : OTTHUMG00000171083
ProteinUniProt: P59768
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNG2
BioGPS: 54331
Gene Expression Atlas: ENSG00000186469
The Human Protein Atlas: ENSG00000186469
PathwayNCI Pathway Interaction Database: GNG2
KEGG: GNG2
REACTOME: GNG2
ConsensusPathDB
Pathway Commons: GNG2
MetabolismMetaCyc: GNG2
HUMANCyc: GNG2
RegulationEnsembl's Regulation: ENSG00000186469
miRBase: chr14 :52,327,021-52,436,518
TargetScan: NM_001243773
cisRED: ENSG00000186469
ContextiHOP: GNG2
cancer metabolism search in PubMed: GNG2
UCL Cancer Institute: GNG2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GNG2 in cancer cell metabolism1. Matimba A, Li F, Livshits A, Cartwright CS, Scully S, et al. (2014) Thiopurine pharmacogenomics: association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics 15: 433-447. doi: 10.2217/pgs.13.226. pmid: 4027966. go to article
2. Yajima I, Kumasaka MY, Tamura H, Ohgami N, Kato M (2012) Functional analysis of GNG2 in human malignant melanoma cells. J Dermatol Sci 68: 172-178. doi: 10.1016/j.jdermsci.2012.09.009. go to article

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Phenotypic Information for GNG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNG2
Familial Cancer Database: GNG2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 606981; gene.
Orphanet
DiseaseKEGG Disease: GNG2
MedGen: GNG2 (Human Medical Genetics with Condition)
ClinVar: GNG2
PhenotypeMGI: GNG2 (International Mouse Phenotyping Consortium)
PhenomicDB: GNG2

Mutations for GNG2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GNG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF886210GNG218144145243579152435921GNG2139192145243584452435897

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4     2 1 1      
GAIN (# sample)4     2 1        
LOSS (# sample)          1      
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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check002.gifSNV 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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=1)
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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr14:52433367-52433367p.P60S5
chr14:52433353-52433353p.P55L3
chr14:52433368-52433368p.P60L1
chr14:52417415-52417415p.A7T1
chr14:52433384-52433384p.K65N1
chr14:52417471-52417471p.I25I1
chr14:52433399-52433399p.I70I1
chr14:52417474-52417474p.D26E1
chr14:52433402-52433402p.L71L1
chr14:52417477-52417477p.R27S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1   1      4    5  2
# mutation1   1      4    3  2
nonsynonymous SNV1   1      4    1  2
synonymous SNV                2   
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr14:52433367p.P60S,GNG23
chr14:52433353p.P55L,GNG22
chr14:52417474p.D26E,GNG21
chr14:52417477p.R27S,GNG21
chr14:52433295p.D36Y,GNG21
chr14:52433336p.P49P,GNG21
chr14:52433361p.E58Q,GNG21
chr14:52433368p.P60L,GNG21
chr14:52433384p.K65N,GNG21
chr14:52433399p.I70I,GNG21

check002.gifOther 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

check002.gifCopy Number for GNG2 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 GNG2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

APBB1IP,CD200R1,CELF2,DOCK11,ETS1,EVI2A,FLI1,
FMNL3,GAB3,GIMAP6,GNG2,KCTD12,LIX1L,MPEG1,
PRDM8,RASSF2,SH2B3,SLC9A9,SRGN,WIPF1,ZEB2
ANXA5,ASPH,BHMT2,CAV1,CHRDL1,DOCK11,GNG2,
GNS,ITGB1BP1,ITIH5,ITSN1,LAMA4,PALMD,PCDH9,
PYGL,RHOQ,SAR1A,SEPT11,SORBS1,STS,VKORC1L1

ARHGEF6,CYSLTR1,DOCK10,FLI1,GIMAP4,GIMAP6,GIMAP7,
GNG2,GYPC,ITGA4,LRRC8C,MYO5A,PPP1R16B,PRKCB,
RASSF2,RCSD1,SH2D3C,SLC9A9,SYT11,WIPF1,ZIK1
AGTR1,AP1S2,BAI3,BCHE,CADM1,CEND1,CRISPLD1,
DDIT4L,DGKB,EID2B,FAM171B,GLRB,GNG2,GYG1,
NECAB1,NUDT10,SGCE,SH3BGRL,SSBP2,ZDHHC15,ZDHHC22
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 GNG2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28784; -.
Organism-specific databasesCTD 54331; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01159guanine nucleotide binding protein (G protein), gamma 2approvedHalothane
DB00125guanine nucleotide binding protein (G protein), gamma 2approved; nutraceuticalL-Arginine
DB00435guanine nucleotide binding protein (G protein), gamma 2approvedNitric Oxide


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Cross referenced IDs for GNG2
* 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



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