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 ARFGEF2
Basic gene info.Gene symbolARFGEF2
Gene nameADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)
SynonymsBIG2|PVNH2|dJ1164I10.1
CytomapUCSC genome browser: 20q13.13
Genomic locationchr20 :47538274-47653230
Type of geneprotein-coding
RefGenesNM_006420.2,
Ensembl idENSG00000124198
Descriptionbrefeldin A-inhibited GEP 2brefeldin A-inhibited guanine nucleotide-exchange protein 2
Modification date20141207
dbXrefs MIM : 605371
HGNC : HGNC
Ensembl : ENSG00000124198
HPRD : 09250
Vega : OTTHUMG00000032687
ProteinUniProt: Q9Y6D5
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARFGEF2
BioGPS: 10564
Gene Expression Atlas: ENSG00000124198
The Human Protein Atlas: ENSG00000124198
PathwayNCI Pathway Interaction Database: ARFGEF2
KEGG: ARFGEF2
REACTOME: ARFGEF2
ConsensusPathDB
Pathway Commons: ARFGEF2
MetabolismMetaCyc: ARFGEF2
HUMANCyc: ARFGEF2
RegulationEnsembl's Regulation: ENSG00000124198
miRBase: chr20 :47,538,274-47,653,230
TargetScan: NM_006420
cisRED: ENSG00000124198
ContextiHOP: ARFGEF2
cancer metabolism search in PubMed: ARFGEF2
UCL Cancer Institute: ARFGEF2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ARFGEF2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ARFGEF2
Familial Cancer Database: ARFGEF2
* 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 605371; gene.
608097; phenotype.
Orphanet 98892; Periventricular nodular heterotopia.
DiseaseKEGG Disease: ARFGEF2
MedGen: ARFGEF2 (Human Medical Genetics with Condition)
ClinVar: ARFGEF2
PhenotypeMGI: ARFGEF2 (International Mouse Phenotyping Consortium)
PhenomicDB: ARFGEF2

Mutations for ARFGEF2
* 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
ovaryARFGEF2chr204756796947567989BCAS3chr175920634159206361
ovaryARFGEF2chr204763431947634339ARFGEF2chr204760128447601304
pancreasARFGEF2chr204756944647569466ARFGEF2chr204757002347570043
pancreasARFGEF2chr204758891447588934chr204811388648113906
pancreasARFGEF2chr204759206647592086ARFGEF2chr204759235247592372
pancreasARFGEF2chr204762603747626057ARFGEF2chr204762614247626162
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 ARFGEF2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW752522ARFGEF213203204758765747587847TMED11P189491411103601110662

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 # sample6       1 1      
GAIN (# sample)6       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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=145)
Stat. for Synonymous SNVs
(# total SNVs=35)
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
chr20:47605048-47605048p.K794K4
chr20:47587670-47587670p.R402C4
chr20:47570297-47570297p.A270T3
chr20:47588912-47588912p.S492Y3
chr20:47605046-47605046p.K794E3
chr20:47585760-47585760p.R379H3
chr20:47570183-47570183p.R232C3
chr20:47630449-47630449p.I1377I2
chr20:47607631-47607631p.S957G2
chr20:47630457-47630457p.R1380P2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample464223 7 5311351  2420317
# mutation465214 7 5311361  2625329
nonsynonymous SNV454173 4 32 951  1821323
synonymous SNV 1141 3 21141   84 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
chr20:47605048p.K794K4
chr20:47570297p.E1170K2
chr20:47639640p.S492Y2
chr20:47570183p.R232C2
chr20:47621682p.A270T2
chr20:47588912p.L1559F2
chr20:47606137p.K1575T1
chr20:47626856p.T793R1
chr20:47639592p.F951L1
chr20:47591403p.N103N1

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 ARFGEF2 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 ARFGEF2

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

ADNP,APOOL,ARFGEF2,ATP9A,C12orf66,SOGA1,CHD6,
CSE1L,DDI2,LOC647979,LRBA,NCOA3,PDPK1,LTN1,
RSC1A1,SBNO1,SERINC3,SS18L1,STAU1,TAF4,WDFY3
AFF4,ARFGEF2,ARID2,AVL9,BIRC6,CCDC186,CDK12,
CLCN3,KDM6A,LATS1,MYSM1,KAT6B,N4BP2,NCOA2,
NF1,NIPBL,RAPGEF6,SLC25A40,SLC35A3,WAPAL,ZNF678

ADNP,ARFGEF2,ASXL1,ATP9A,NOL4L,FAM217B,DIDO1,
ITCH,KIF3B,LOC647979,NCOA3,NCOA6,PHF20,PLAGL2,
POFUT1,PPP1R3D,PXMP4,RALGAPB,RPRD1B,STAU1,TAF4
ARFGEF1,ARFGEF2,ARHGAP32,PRR14L,CNOT1,DNAJC16,FGD4,
FRYL,GUF1,LARP4B,MCTP2,MED14,MYO10,NBEAL1,
PAWR,PLCE1,PLEKHH1,PRSS12,TET3,ZCCHC6,ZDHHC23
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 ARFGEF2


There's no related Drug.
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Cross referenced IDs for ARFGEF2
* 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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