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 GGPS1
Basic gene info.Gene symbolGGPS1
Gene namegeranylgeranyl diphosphate synthase 1
SynonymsGGPPS|GGPPS1
CytomapUCSC genome browser: 1q43
Genomic locationchr1 :235491752-235507844
Type of geneprotein-coding
RefGenesNM_001037277.1,
NR_036605.1,NM_001037278.1,NM_004837.3,
Ensembl idENSG00000152904
Description(2E,6E)-farnesyl diphosphate synthaseGGPP synthaseGGPPSasedimethylallyltranstransferasefarnesyl diphosphate synthasefarnesyltranstransferasegeranylgeranyl pyrophosphate synthasegeranyltranstransferase
Modification date20141207
dbXrefs MIM : 606982
HGNC : HGNC
Ensembl : ENSG00000152904
HPRD : 06099
Vega : OTTHUMG00000037963
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GGPS1
BioGPS: 9453
Gene Expression Atlas: ENSG00000152904
The Human Protein Atlas: ENSG00000152904
PathwayNCI Pathway Interaction Database: GGPS1
KEGG: GGPS1
REACTOME: GGPS1
ConsensusPathDB
Pathway Commons: GGPS1
MetabolismMetaCyc: GGPS1
HUMANCyc: GGPS1
RegulationEnsembl's Regulation: ENSG00000152904
miRBase: chr1 :235,491,752-235,507,844
TargetScan: NM_001037277
cisRED: ENSG00000152904
ContextiHOP: GGPS1
cancer metabolism search in PubMed: GGPS1
UCL Cancer Institute: GGPS1
Assigned class in ccmGDBC

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Phenotypic Information for GGPS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GGPS1
Familial Cancer Database: GGPS1
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GGPS1
MedGen: GGPS1 (Human Medical Genetics with Condition)
ClinVar: GGPS1
PhenotypeMGI: GGPS1 (International Mouse Phenotyping Consortium)
PhenomicDB: GGPS1

Mutations for GGPS1
* 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 GGPS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA325909GGPS111131235492854235492966INO80B11243327468646074686780
Z21101GGPS1182051235491905235492093PBRM120139435271421852721371
DB026779RBM3412521235324208235324565GGPS12535661235498557235505475
DA612754ARID4B14391235490229235491471GGPS14385941235498555235505084

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
There's no copy number variation information in COSMIC data for this gene.

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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=22)		Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=2)		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
chr1:235505887-235505887p.R235C3
chr1:235505467-235505467p.V95M2
chr1:235498595-235498595p.E6K2
chr1:235505913-235505913p.K245fs*102
chr1:235505712-235505712p.L176L2
chr1:235505745-235505745p.R187R1
chr1:235506071-235506071p.K296I1
chr1:235505413-235505413p.P77S1
chr1:235505756-235505756p.A191D1
chr1:235505444-235505444p.S87C1

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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 1 2       221  11 4
# mutation 1 2       221  11 4
nonsynonymous SNV   2       221  11 2
synonymous SNV 1                 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
chr1:235505796p.S214L1
chr1:235505820p.S214S1
chr1:235505825p.G280W1
chr1:235498582p.K296I1
chr1:235505826p.M1I1
chr1:235498608p.R10I1
chr1:235506022p.D65H1
chr1:235505377p.A111S1
chr1:235506071p.A111V1
chr1:235505515p.P175P1

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 GGPS1 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 GGPS1

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

ANGEL2,ARID4B,ARV1,C1orf27,LINC00467,COG2,FBXO28,
GGPS1,GNPAT,HNRNPU,LYPLAL1,NSL1,RBM34,SRP9,
TBCE,TFB2M,TMCO1,TOMM20,TROVE2,TSNAX,WDR26		ARV1,GSKIP,C18orf32,CCNC,GGPS1,GOLPH3,IER3IP1,
JKAMP,LSM12,MRPL50,PSMD10,RAB11A,RAB14,SCOC,
SELT,SRP9,SUMO1,TMCO1,TMEM59,TXNDC9,UBE2N

METTL18,TRMT1L,C1orf27,C1orf43,COG2,GGPS1,GNPAT,
JTB,MRPS14,PIGC,PRUNE,RBM34,RFWD2,SPHAR,
SRP9,TIPRL,TOMM20,TROVE2,TSNAX,UFC1,VPS72		ANAPC16,BTF3L4,FAM204A,C11orf58,BRK1,COPS2,SMIM11,
FUNDC2,GGPS1,POLR2M___GCOM1,METTL5,MRFAP1L1,PAIP1,PCNP,
PRKRA,RAB33B,RYK,TCEAL8,UBE2Q2,ZCRB1,ZNF32
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 GGPS1
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
DB00399geranylgeranyl diphosphate synthase 1approvedZoledronate
DB02552geranylgeranyl diphosphate synthase 1experimentalGeranyl Diphosphate
DB04695geranylgeranyl diphosphate synthase 1experimentalFARNESYL THIOPYROPHOSPHATE
DB04714geranylgeranyl diphosphate synthase 1experimentalISOPENTENYL PYROPHOSPHATE
DB06830geranylgeranyl diphosphate synthase 1experimental(1-HYDROXYHEPTANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
DB06931geranylgeranyl diphosphate synthase 1experimental(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
DB07221geranylgeranyl diphosphate synthase 1experimental(2,2-DIPHOSPHONOETHYL)(DODECYL)DIMETHYLPHOSPHONIUM
DB07410geranylgeranyl diphosphate synthase 1experimental[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID
DB07780geranylgeranyl diphosphate synthase 1experimentalFARNESYL DIPHOSPHATE
DB07841geranylgeranyl diphosphate synthase 1experimentalGERANYLGERANYL DIPHOSPHATE
DB07873geranylgeranyl diphosphate synthase 1experimental(1-HYDROXYDODECANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
DB08529geranylgeranyl diphosphate synthase 1experimental(6E,11E)-HEPTADECA-6,11-DIENE-9,9-DIYLBIS(PHOSPHONIC ACID)


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Cross referenced IDs for GGPS1
* 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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