Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	ARFGEF2
	Gene name	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)
	Synonyms	BIG2\|PVNH2\|dJ1164I10.1
	Cytomap	UCSC genome browser: 20q13.13
	Genomic location	chr20 :47538274-47653230
	Type of gene	protein-coding
	RefGenes	NM_006420.2,
	Ensembl id	ENSG00000124198
	Description	brefeldin A-inhibited GEP 2brefeldin A-inhibited guanine nucleotide-exchange protein 2
	Modification date	20141207
dbXrefs	MIM : 605371
	HGNC : HGNC
	Ensembl : ENSG00000124198
	HPRD : 09250
	Vega : OTTHUMG00000032687
Protein	UniProt: Q9Y6D5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARFGEF2
	BioGPS: 10564
	Gene Expression Atlas: ENSG00000124198
	The Human Protein Atlas: ENSG00000124198
Pathway	NCI Pathway Interaction Database: ARFGEF2
	KEGG: ARFGEF2
	REACTOME: ARFGEF2
	ConsensusPathDB
	Pathway Commons: ARFGEF2
Metabolism	MetaCyc: ARFGEF2
	HUMANCyc: ARFGEF2
Regulation	Ensembl's Regulation: ENSG00000124198
	miRBase: chr20 :47,538,274-47,653,230
	TargetScan: NM_006420
	cisRED: ENSG00000124198
Context	iHOP: ARFGEF2
	cancer metabolism search in PubMed: ARFGEF2
	UCL Cancer Institute: ARFGEF2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ARFGEF2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	605371; gene. 608097; phenotype.
Orphanet	98892; Periventricular nodular heterotopia.
Disease	KEGG Disease: ARFGEF2
	MedGen: ARFGEF2 (Human Medical Genetics with Condition)
	ClinVar: ARFGEF2
Phenotype	MGI: ARFGEF2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ARFGEF2	chr20	47567969	47567989	BCAS3	chr17	59206341	59206361
ovary	ARFGEF2	chr20	47634319	47634339	ARFGEF2	chr20	47601284	47601304
pancreas	ARFGEF2	chr20	47569446	47569466	ARFGEF2	chr20	47570023	47570043
pancreas	ARFGEF2	chr20	47588914	47588934		chr20	48113886	48113906
pancreas	ARFGEF2	chr20	47592066	47592086	ARFGEF2	chr20	47592352	47592372
pancreas	ARFGEF2	chr20	47626037	47626057	ARFGEF2	chr20	47626142	47626162

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ARFGEF2 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

AW752522

ARFGEF2

203

47587657

47587847

TMED11P

189

491

1110360

1110662

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr20:47605048-47605048	p.K794K	4
chr20:47587670-47587670	p.R402C	4
chr20:47585760-47585760	p.R379H	3
chr20:47605046-47605046	p.K794E	3
chr20:47570183-47570183	p.R232C	3
chr20:47570297-47570297	p.A270T	3
chr20:47588912-47588912	p.S492Y	3
chr20:47626806-47626806	p.A1208S	2
chr20:47645144-47645144	p.R1668*	2
chr20:47632850-47632850	p.A1405T	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	4	6	4	22	3		7		5	3	1	13	5	1			24	20	3	17
# mutation	4	6	5	21	4		7		5	3	1	13	6	1			26	25	3	29
nonsynonymous SNV	4	5	4	17	3		4		3	2		9	5	1			18	21	3	23
synonymous SNV		1	1	4	1		3		2	1	1	4	1				8	4		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr20:47605048	p.K794K	4
chr20:47570183	p.A270T	2
chr20:47588912	p.L1559F	2
chr20:47621682	p.E1170K	2
chr20:47570297	p.S492Y	2
chr20:47639640	p.R232C	2
chr20:47587733	p.D1083N	1
chr20:47604875	p.N1224N	1
chr20:47614755	p.R423G	1
chr20:47630428	p.W1370C	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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