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 RAPGEF4
Basic gene info.Gene symbolRAPGEF4
Gene nameRap guanine nucleotide exchange factor (GEF) 4
Synonyms2|CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496
CytomapUCSC genome browser: 2q31-q32
Genomic locationchr2 :173686314-173917620
Type of geneprotein-coding
RefGenesNM_001100397.1,
NM_001282899.1,NM_001282900.1,NM_001282901.1,NM_007023.3,
Ensembl idENSG00000091428
DescriptionRAP guanine-nucleotide-exchange factor (GEF) 4cAMP-regulated guanine nucleotide exchange factor IIexchange factor directly activated by cAMP 2exchange protein directly activated by cAMP 2putative protein product of Nbla00496rap guanine nucleotide exc
Modification date20141207
dbXrefs MIM : 606058
HGNC : HGNC
Ensembl : ENSG00000091428
HPRD : 06929
Vega : OTTHUMG00000133677
ProteinUniProt: Q8WZA2
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAPGEF4
BioGPS: 11069
Gene Expression Atlas: ENSG00000091428
The Human Protein Atlas: ENSG00000091428
PathwayNCI Pathway Interaction Database: RAPGEF4
KEGG: RAPGEF4
REACTOME: RAPGEF4
ConsensusPathDB
Pathway Commons: RAPGEF4
MetabolismMetaCyc: RAPGEF4
HUMANCyc: RAPGEF4
RegulationEnsembl's Regulation: ENSG00000091428
miRBase: chr2 :173,686,314-173,917,620
TargetScan: NM_001100397
cisRED: ENSG00000091428
ContextiHOP: RAPGEF4
cancer metabolism search in PubMed: RAPGEF4
UCL Cancer Institute: RAPGEF4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RAPGEF4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RAPGEF4
Familial Cancer Database: RAPGEF4
* 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 606058; gene.
Orphanet
DiseaseKEGG Disease: RAPGEF4
MedGen: RAPGEF4 (Human Medical Genetics with Condition)
ClinVar: RAPGEF4
PhenotypeMGI: RAPGEF4 (International Mouse Phenotyping Consortium)
PhenomicDB: RAPGEF4

Mutations for RAPGEF4
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryRAPGEF4chr2173733183173733203chr2173561842173561862
ovaryRAPGEF4chr2173733966173733986chr2228710130228710150
ovaryRAPGEF4chr2173734082173734102TBC1D1chr43812985338129873
ovaryRAPGEF4chr2173866226173866246RAPGEF4chr2173859971173859991
pancreasRAPGEF4chr2173915560173915580chr2194419537194419557
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RAPGEF4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF962288DGKI14587137466791137466835RAPGEF4562192173901377173916432
BP342773RAPGEF414932173792880173832125PGA3484582116097104560971629
BF762844ARID1B123926157301568157301948RAPGEF43734472173765015173765255

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 # sample1       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=83)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=2)
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
chr2:173882186-173882186p.G654G2
chr2:173894979-173894979p.W882C2
chr2:173891893-173891893p.E822K2
chr2:173883534-173883534p.?2
chr2:173662258-173662258p.R72C2
chr2:173881108-173881108p.R614Q2
chr2:173853466-173853466p.A425S2
chr2:173850190-173850190p.I373M2
chr2:173881122-173881122p.L619I2
chr2:173853487-173853487p.R432*2

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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
# sample42 111   21 871 1157 19
# mutation42 151   21 881 1178 21
nonsynonymous SNV41 81   11 771 1116 15
synonymous SNV 1 7    1  11   62 6
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
chr2:173679007p.G434G,RAPGEF42
chr2:173850190p.D100Y2
chr2:173882186p.R29R,RAPGEF42
chr2:173787010p.I153I,RAPGEF42
chr2:173883386p.D23D,RAPGEF41
chr2:173832042p.A205S,RAPGEF41
chr2:173853466p.P404S,RAPGEF41
chr2:173891404p.E566E,RAPGEF41
chr2:173659880p.R768R,RAPGEF41
chr2:173879257p.E65K1

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 RAPGEF4 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 RAPGEF4

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

ATF7,BAZ2B,BMPR2,C4orf32,KIAA0825,CYBRD1,DIXDC1,
DYNC1I2,FRY,FZD4,LOC344595,MEGF9,PCTP,RAPGEF4,
RBM43,SYTL2,YPEL2,ZAK,ZNF280D,ZNF484,ZNF510
ARID4A,ATF2,ATF7,BAG4,BTBD8,CAPRIN2,CDADC1,
CDC14B,KIAA1107,LPHN2,MGEA5,ICE2,PKN2,RAPGEF4,
RFC1,RIC8B,SMEK2,TRPM7,TTC3,ZC3H7A,ZNF391

APH1B,BCAM,DACH1,EMID1,EPB41L5,F10,FARP1,
FREM2,IPW,LOC91149,NKD1,PPAP2B,RAPGEF4,SAMD14,
SCT,SLC38A3,SOX5,TNFRSF19,TRIM71,TXLNB,ZFYVE16
ANGPT2,CCL14,CLEC1A,CSGALNACT1,CYYR1,ELTD1,EMCN,
ERG,FAM13C,FAM198B,GPR116,LDB2,LOC100190938,MYCT1,
PECAM1,PLCXD3,RAPGEF4,RSPO3,TEK,TFPI,TGFBR2
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 RAPGEF4
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q8WZA2; -.
ChemistryChEMBL CHEMBL2029198; -.
ChemistryGuidetoPHARMACOLOGY 1293; -.
Organism-specific databasesPharmGKB PA134861108; -.
Organism-specific databasesCTD 11069; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01124Rap guanine nucleotide exchange factor (GEF) 4approvedTolbutamide


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Cross referenced IDs for RAPGEF4
* 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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