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 GNA11
Basic gene info.Gene symbolGNA11
Gene nameguanine nucleotide binding protein (G protein), alpha 11 (Gq class)
SynonymsFBH|FBH2|FHH2|GNA-11|HHC2|HYPOC2
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :3094407-3121454
Type of geneprotein-coding
RefGenesNM_002067.4,
Ensembl idENSG00000088256
DescriptionG-protein subunit alpha-11g alpha-11guanine nucleotide-binding protein G(y) subunit alphaguanine nucleotide-binding protein subunit alpha-11
Modification date20141222
dbXrefs MIM : 139313
HGNC : HGNC
Ensembl : ENSG00000088256
HPRD : 00759
Vega : OTTHUMG00000180631
ProteinUniProt: P29992
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNA11
BioGPS: 2767
Gene Expression Atlas: ENSG00000088256
The Human Protein Atlas: ENSG00000088256
PathwayNCI Pathway Interaction Database: GNA11
KEGG: GNA11
REACTOME: GNA11
ConsensusPathDB
Pathway Commons: GNA11
MetabolismMetaCyc: GNA11
HUMANCyc: GNA11
RegulationEnsembl's Regulation: ENSG00000088256
miRBase: chr19 :3,094,407-3,121,454
TargetScan: NM_002067
cisRED: ENSG00000088256
ContextiHOP: GNA11
cancer metabolism search in PubMed: GNA11
UCL Cancer Institute: GNA11
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GNA11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNA11
Familial Cancer Database: GNA11
* 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 139313; gene.
145981; phenotype.
615361; phenotype.
Orphanet 101049; Familial hypocalciuric hypercalcemia type 2.
428; Autosomal dominant hypocalcemia.
DiseaseKEGG Disease: GNA11
MedGen: GNA11 (Human Medical Genetics with Condition)
ClinVar: GNA11
PhenotypeMGI: GNA11 (International Mouse Phenotyping Consortium)
PhenomicDB: GNA11

Mutations for GNA11
* 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 GNA11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK818891GNA1112161931150363119254REG1A20826027935048379350535
CK818890REG1A166427935048379350531GNA11562721931150353119254
BM126302GNA1112001931150523119254REG1A19224427935048379350535
BM126025REG1A126427935048379350535GNA11562251931189333119254

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 # sample   1 1           
GAIN (# sample)     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=261

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=279)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr19:3118942-3118942p.Q209L143
chr19:3115012-3115012p.R183C9
chr19:3118942-3118943p.Q209L4
chr19:3118941-3118941p.Q209K4
chr19:3115011-3115012p.R183C3
chr19:3113468-3113468p.S154S2
chr19:3113330-3113330p.A108A2
chr19:3115013-3115013p.R183L2
chr19:3113410-3113410p.L135P1
chr19:3121014-3121014p.R306L1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  171   1  311  77 3
# mutation  171   1  411  77 3
nonsynonymous SNV  14    1  311  45 2
synonymous SNV   31      1    32 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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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
chr19:3113330p.A108A2
chr19:3115013p.I56M1
chr19:3119342p.S211S1
chr19:3110205p.L351P1
chr19:3115036p.K57Q1
chr19:3119345p.I217I1
chr19:3110206p.A65A1
chr19:3118923p.V223A1
chr19:3121014p.G66S1
chr19:3110298p.L229V1

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 GNA11 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 GNA11

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

AP3D1,PRRC2B,NOP9,C9orf129,CASZ1,CCNT1,DDI2,
GIGYF2,GNA11,HCFC1,HERC2,LMTK2,KMT2B___KMT2D,NACC2,
NFIC,PRKAR2A,RREB1,TGFBRAP1,TRIM56,YLPM1,ZNF641
ANKRD11,ATG2A,PRRC2A,PRRC2B,GATC,GCN1L1,GLYR1,
GNA11,HERC2,KHSRP,ZSWIM8,NCOR2,OTUD7A,PHF2,
POLR3E,PRDM11,RNF216,RPTOR,SUPT6H,TECPR2,ZC3H7B

BTNL8,C9orf129,CNNM4,CORO2A,GNA11,GPT,GUCA2B,
JOSD1,KIAA1161,LRP10,LUZP1,NBEAL1,PEX26,PHLPP2,
PLEKHA7,PTPRH,RGP1,RREB1,SLC9A1,TTC22,ZZEF1
AGPAT3,MISP,C1orf106,CARD10,COBL,GNA11,KCNK5,
KIAA0247,LASP1,LPIN2,LUZP1,MALL,MAST2,MYO5B,
MYO7B,PLEKHG6,SCIN,SLC9A3R1,SORT1,SPINT1,TOM1
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 GNA11
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28764; -.
Organism-specific databasesCTD 2767; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125guanine nucleotide binding protein (G protein), alpha 11 (Gq class)approved; nutraceuticalL-Arginine
DB00435guanine nucleotide binding protein (G protein), alpha 11 (Gq class)approvedNitric Oxide


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Cross referenced IDs for GNA11
* 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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