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 RAPGEF3
Basic gene info.Gene symbolRAPGEF3
Gene nameRap guanine nucleotide exchange factor (GEF) 3
SynonymsCAMP-GEFI|EPAC|EPAC1|HSU79275|bcm910
CytomapUCSC genome browser: 12q13.1
Genomic locationchr12 :48128452-48152889
Type of geneprotein-coding
RefGenesNM_001098531.2,
NM_001098532.2,NM_006105.5,
Ensembl idENSG00000079337
Description9330170P05RikEPAC 1Rap1 guanine-nucleotide-exchange factor directly activated by cAMPcAMP-regulated guanine nucleotide exchange factor Iexchange factor directly activated by cAMP 1exchange protein directly activated by cAMP 1rap guanine nucleotide e
Modification date20141207
dbXrefs MIM : 606057
HGNC : HGNC
Ensembl : ENSG00000079337
HPRD : 06928
Vega : OTTHUMG00000133667
ProteinUniProt: O95398
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAPGEF3
BioGPS: 10411
Gene Expression Atlas: ENSG00000079337
The Human Protein Atlas: ENSG00000079337
PathwayNCI Pathway Interaction Database: RAPGEF3
KEGG: RAPGEF3
REACTOME: RAPGEF3
ConsensusPathDB
Pathway Commons: RAPGEF3
MetabolismMetaCyc: RAPGEF3
HUMANCyc: RAPGEF3
RegulationEnsembl's Regulation: ENSG00000079337
miRBase: chr12 :48,128,452-48,152,889
TargetScan: NM_001098531
cisRED: ENSG00000079337
ContextiHOP: RAPGEF3
cancer metabolism search in PubMed: RAPGEF3
UCL Cancer Institute: RAPGEF3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RAPGEF3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RAPGEF3
Familial Cancer Database: RAPGEF3
* 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 606057; gene.
Orphanet
DiseaseKEGG Disease: RAPGEF3
MedGen: RAPGEF3 (Human Medical Genetics with Condition)
ClinVar: RAPGEF3
PhenotypeMGI: RAPGEF3 (International Mouse Phenotyping Consortium)
PhenomicDB: RAPGEF3

Mutations for RAPGEF3
* 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 RAPGEF3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF841153ZNF43618712368690423686990RAPGEF380193124814005348140166

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             
GAIN (# sample)   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=49)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:48132517-48132517p.G786R3
chr12:48141501-48141501p.F447F2
chr12:48142692-48142692p.R313Q2
chr12:48143716-48143716p.V230M2
chr12:48137388-48137388p.E542*2
chr12:48134776-48134776p.G615G2
chr12:48142636-48142636p.G332S2
chr12:48144140-48144140p.A205V1
chr12:48134142-48134142p.A714A1
chr12:48141893-48141893p.M387K1

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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   111 6 31 71   155 9
# mutation   111 6 31 71   166 9
nonsynonymous SNV   91 4 21 5    93 9
synonymous SNV   2  2 1  21   73  
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
chr12:48134566p.L875I,RAPGEF31
chr12:48143587p.P688P,RAPGEF31
chr12:48137435p.P442L,RAPGEF31
chr12:48151769p.D236N,RAPGEF31
chr12:48132947p.R874H,RAPGEF31
chr12:48142635p.R655Q,RAPGEF31
chr12:48134707p.D441D,RAPGEF31
chr12:48143716p.G235G,RAPGEF31
chr12:48137448p.S844L,RAPGEF31
chr12:48132950p.S638S,RAPGEF31

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 RAPGEF3 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 RAPGEF3

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

ADCY4,AVPR2,CIRBP,CLDN5,D2HGDH,GPIHBP1,GPR146,
FAM110D,HDAC7,JMJD7-PLA2G4B,KANK3,MYO15B,NEIL1,PHF1,
PNPLA2,RAPGEF3,SRSF5,TENC1,TMEM88,TPO,USHBP1
ADCY4,ARHGEF15,BTNL9,CCM2L,CYGB,FAM65C,GNAZ,
GPIHBP1,KANK3,MAP3K3,NOTCH4,NOVA2,PDE2A,PRCD,
RAPGEF3,ROBO4,SCARF1,SHANK3,TENC1,TIE1,USHBP1

AHNAK,BHLHE41,C10orf54,MIR22HG,CD59,CDKN2B,CYTH1,
DGKA,GSN,FAM214B,LYST,MCOLN1,MEGF6,MMP28,
PINK1,RAPGEF3,ST6GALNAC6,TNKS1BP1,TRANK1,TRIM8,ZFYVE28
ADAMTS10,ADAMTS6,ADCY4,APCDD1,BTNL9,FBF1,GJA4,
HSPA7,ITGBL1,ITIH4,MAP3K12,MEG3,MTMR9LP,NOTCH4,
PCOLCE,PEAR1,RAPGEF3,RCN3,SLC25A27,TDRD10,USHBP1
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 RAPGEF3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2029197; -.
Organism-specific databasesPharmGKB PA134910959; -.
Organism-specific databasesCTD 10411; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171Rap guanine nucleotide exchange factor (GEF) 3approved; nutraceuticalAdenosine triphosphate
DB00770Rap guanine nucleotide exchange factor (GEF) 3approved; investigationalAlprostadil
DB00668Rap guanine nucleotide exchange factor (GEF) 3approvedEpinephrine


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Cross referenced IDs for RAPGEF3
* 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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