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 GRP
Basic gene info.Gene symbolGRP
Gene namegastrin-releasing peptide
SynonymsBN|GRP-10|preproGRP|proGRP
CytomapUCSC genome browser: 18q21.1-q21.32
Genomic locationchr18 :56887399-56898002
Type of geneprotein-coding
RefGenesNM_001012512.1,
NM_001012513.1,NM_002091.3,
Ensembl idENSG00000134443
Descriptionbombesinneuromedin Cpre-progastrin releasing peptideprepro-GRP
Modification date20141222
dbXrefs MIM : 137260
HGNC : HGNC
Ensembl : ENSG00000134443
HPRD : 08845
Vega : OTTHUMG00000132760
ProteinUniProt: P07492
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GRP
BioGPS: 2922
Gene Expression Atlas: ENSG00000134443
The Human Protein Atlas: ENSG00000134443
PathwayNCI Pathway Interaction Database: GRP
KEGG: GRP
REACTOME: GRP
ConsensusPathDB
Pathway Commons: GRP
MetabolismMetaCyc: GRP
HUMANCyc: GRP
RegulationEnsembl's Regulation: ENSG00000134443
miRBase: chr18 :56,887,399-56,898,002
TargetScan: NM_001012512
cisRED: ENSG00000134443
ContextiHOP: GRP
cancer metabolism search in PubMed: GRP
UCL Cancer Institute: GRP
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GRP in cancer cell metabolism1. Rellinger EJ, Romain C, Choi S, Qiao J, Chung DH (2015) Silencing gastrin-releasing peptide receptor suppresses key regulators of aerobic glycolysis in neuroblastoma cells. Pediatr Blood Cancer 62: 581-586. doi: 10.1002/pbc.25348. pmid: 4339541. go to article

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Phenotypic Information for GRP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GRP
Familial Cancer Database: GRP
* 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 137260; gene.
Orphanet
DiseaseKEGG Disease: GRP
MedGen: GRP (Human Medical Genetics with Condition)
ClinVar: GRP
PhenotypeMGI: GRP (International Mouse Phenotyping Consortium)
PhenomicDB: GRP

Mutations for GRP
* 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 GRP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=13

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=6)
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
chr18:56887507-56887507p.R4S13
chr18:56897675-56897678p.R141fs*46
chr18:56892843-56892843p.L87F1
chr18:56897691-56897691p.N146K1
chr18:56887632-56887632p.A45A1
chr18:56892885-56892885p.P101T1
chr18:56892727-56892727p.H48R1
chr18:56892886-56892886p.P101L1
chr18:56892729-56892729p.L49V1
chr18:56892889-56892889p.K102R1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 4  1    1    22  
# mutation 1 4  1    1    22  
nonsynonymous SNV 1 3  1    1    22  
synonymous SNV   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
chr18:56892772p.L49V,GRP1
chr18:56892828p.T55A,GRP1
chr18:56892843p.E63A,GRP1
chr18:56892885p.R82R,GRP1
chr18:56892886p.L87F,GRP1
chr18:56892918p.P101T,GRP1
chr18:56892961p.P101L,GRP1
chr18:56897646p.D112N,GRP1
chr18:56897691p.G126D,GRP1
chr18:56892729p.S125C1

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 GRP 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 GRP

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

ANKHD1,SPDL1,CDC23,ETF1,G3BP1,GRPEL2,HMMR,
HSPA9,LARP1,LARS,NPM1,RARS,RBM22,RBM27,
SRSF10,SRSF1,SMAD5,TCERG1,UBE2D2,ZFP62,ZNF354A
C14orf28,C3orf38,C6orf62,RBM48,CCDC117,CGGBP1,GRPEL2,
MSANTD4,NANP,NSL1,RNF219,SREK1IP1,TAF9B,TBL1XR1,
THAP1,TRIM13,ZBTB34,ZBTB6,ZBTB14,ZNF566,ZNF684

PARPBP,CCDC59,CCNB1,CCNH,CCT2,CDK1,CENPK,
GRPEL2,HINT1,MAD2L1,MRPL22,MRPL42,MRPS27,NPM1,
PPP2CA,RIOK2,SREK1IP1,TAF9,TBCA,UBE2N,ZCCHC9
ARL5A,ATG3,BET1,BUD13,CBX3,PBDC1,ENOPH1,
FOXN2,GLO1,GRPEL2,LSM6,OSTC,PEX3,TRMT10A,
RIOK2,SEC22B,SMS,SVIP,UCHL5,ZC3H15,ZCCHC9
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 GRP


There's no related Drug.
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Cross referenced IDs for GRP
* 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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