Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 GGCX
Basic gene info.Gene symbolGGCX
Gene namegamma-glutamyl carboxylase
SynonymsVKCFD1
CytomapUCSC genome browser: 2p12
Genomic locationchr2 :85771977-85788657
Type of geneprotein-coding
RefGenesNM_000821.5,
NM_001142269.2,
Ensembl idENSG00000115486
Descriptionpeptidyl-glutamate 4-carboxylasevitamin K-dependent gamma-carboxylase
Modification date20141222
dbXrefs MIM : 137167
HGNC : HGNC
Ensembl : ENSG00000115486
HPRD : 00665
Vega : OTTHUMG00000130173
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GGCX
BioGPS: 2677
Gene Expression Atlas: ENSG00000115486
The Human Protein Atlas: ENSG00000115486
PathwayNCI Pathway Interaction Database: GGCX
KEGG: GGCX
REACTOME: GGCX
ConsensusPathDB
Pathway Commons: GGCX
MetabolismMetaCyc: GGCX
HUMANCyc: GGCX
RegulationEnsembl's Regulation: ENSG00000115486
miRBase: chr2 :85,771,977-85,788,657
TargetScan: NM_000821
cisRED: ENSG00000115486
ContextiHOP: GGCX
cancer metabolism search in PubMed: GGCX
UCL Cancer Institute: GGCX
Assigned class in ccmGDBC

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

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

Mutations for GGCX
* 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 GGCX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ355482GGCX1729928577814685778430ZFP91294498115838758058387783
L17128ITPRIPL21138161913059919130736GGCX125252228577696785788583
BE073949GGCX120728577960885780185GGCX20326628577956785779630

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          1  
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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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
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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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
chr2:85780131-85780131p.R406R3
chr2:85783303-85783303p.?2
chr2:85777139-85777139p.G732E2
chr2:85780536-85780536p.R325Q2
chr2:85777223-85777223p.R704Q2
chr2:85779652-85779652p.D442E2
chr2:85785695-85785695p.R136Q2
chr2:85777724-85777724p.R680*2
chr2:85777850-85777850p.L638M1
chr2:85782717-85782717p.?1

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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
# sample31 8  1    42   64 11
# mutation31 9  1    42   64 14
nonsynonymous SNV2  8  1    41   43 9
synonymous SNV11 1        1   21 5
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
chr2:85785695p.R79Q,GGCX2
chr2:85778102p.S684Y,GGCX1
chr2:85788077p.L452P,GGCX1
chr2:85779675p.S171F,GGCX1
chr2:85777112p.P670P,GGCX1
chr2:85782649p.R441L,GGCX1
chr2:85778164p.A136A,GGCX1
chr2:85780357p.N648S,GGCX1
chr2:85777153p.P427P,GGCX1
chr2:85783344p.N130K,GGCX1

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 GGCX 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 GGCX

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

ANO10,ARF4,COPB2,COPG1,DAP,EIF2AK3,FAM98A,
G6PD,GGCX,GLB1,IMMT,KDELR2,RAB1A,RETSAT,
SLC31A1,SURF4,TEX261,TMEM214,TMEM86A,TP53INP2,CHMP3
ABCB6,ACACA,AGPAT3,ANO10,BRI3BP,C9orf91,COPB2,
COPG1,CRK,FADS2,FAR2,FITM2,GGCX,HFE,
LONP2,NQO1,PAPSS2,SCP2,SLC41A2,SLC5A3,TBC1D24

B3GNT9,CABIN1,CDR2L,DUSP7,FAM63B,FICD,FRRS1,
FUT11,GGCX,HDLBP,LEPRE1,NRBP1,PANX1,PDE4DIP,
PLBD2,PLOD1,SERPINH1,TANC2,TMEM106A,TMEM184B,ZNF70
AARS,ACACA,ALG9,ATXN2,CKAP5,CLPB,DHX29,
GALNT10,GANAB,GGCX,INVS,IPO9,EMC1,LIG3,
LONP2,MAP3K4,MID1IP1,PIK3R4,SPTBN2,UHRF1BP1,XPO7
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 GGCX
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00142gamma-glutamyl carboxylaseapproved; nutraceuticalL-Glutamic Acid
DB00170gamma-glutamyl carboxylaseapproved; nutraceuticalMenadione
DB01022gamma-glutamyl carboxylaseapprovedPhytonadione
DB01125gamma-glutamyl carboxylaseapprovedAnisindione
DB00682gamma-glutamyl carboxylaseapprovedWarfarin


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Cross referenced IDs for GGCX
* 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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