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 ARF3

Basic gene info.	Gene symbol	ARF3
	Gene name	ADP-ribosylation factor 3
	Synonyms	-
	Cytomap	UCSC genome browser: 12q13
	Genomic location	chr12 :49329991-49351252
	Type of gene	protein-coding
	RefGenes	NM_001659.2,
	Ensembl id	ENSG00000134287
	Description	small GTP binding protein
	Modification date	20141207
dbXrefs	MIM : 103190
	HGNC : HGNC
	Ensembl : ENSG00000134287
	HPRD : 00056
	Vega : OTTHUMG00000168080
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARF3
	BioGPS: 377
	Gene Expression Atlas: ENSG00000134287
	The Human Protein Atlas: ENSG00000134287
Pathway	NCI Pathway Interaction Database: ARF3
	KEGG: ARF3
	REACTOME: ARF3
	ConsensusPathDB
	Pathway Commons: ARF3
Metabolism	MetaCyc: ARF3
	HUMANCyc: ARF3
Regulation	Ensembl's Regulation: ENSG00000134287
	miRBase: chr12 :49,329,991-49,351,252
	TargetScan: NM_001659
	cisRED: ENSG00000134287
Context	iHOP: ARF3
	cancer metabolism search in PubMed: ARF3
	UCL Cancer Institute: ARF3
Assigned class in ccmGDB	C

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Phenotypic Information for ARF3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ARF3
	Familial Cancer Database: ARF3

* 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_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ARF3
	MedGen: ARF3 (Human Medical Genetics with Condition)
	ClinVar: ARF3
Phenotype	MGI: ARF3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ARF3

Mutations for ARF3

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ARF3 related fusion information.

ID	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
H14073	GBF1	1	84	10	104142570	104142653	ARF3	76	407	12	49332083	49332407
BF509886	RAD23A	17	192	19	13064281	13064456	ARF3	188	434	12	49331931	49332177
BQ668805	ARF3	1	59	12	49330793	49330851	NDUFA6	60	458	22	42482118	42486691
R23430	ARF3	4	183	12	49332574	49332754	OGFOD2	175	225	12	123463043	123463093
BG001600	ARF3	1	268	12	49332704	49333517	SLC38A7	258	337	16	58700633	58700712
AA527815	ARF3	1	289	12	49331604	49331892	ARF3	284	346	12	49331514	49331576
AI742354	ARF3	1	71	12	49331319	49331389	ARF3	58	342	12	49331518	49331802
R85158	GBF1	1	84	10	104142570	104142653	ARF3	76	276	12	49332083	49332284
AA525008	ARF3	1	289	12	49331604	49331892	ARF3	284	368	12	49331514	49331598
BC020999	CCNB1IP1	1386	2828	14	20779529	20797531	ARF3	2829	3851	12	49332489	49351235
H38464	GBF1	1	84	10	104142570	104142653	ARF3	76	350	12	49332083	49332356
BQ331543	ARF3	22	240	12	49333782	49334840	ITPR2	234	508	12	26959676	26959951

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

There's no copy number variation information in COSMIC data for this gene.

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr12:49333815-49333815	p.R75Q	3
chr12:49334854-49334857	p.L8fs*4	1
chr12:49333820-49333820	p.K73K	1
chr12:49333834-49333834	p.G69R	1
chr12:49333860-49333860	p.N60S	1
chr12:49332749-49332749	p.Q176R	1
chr12:49334730-49334730	p.?	1
chr12:49332794-49332794	p.T161I	1
chr12:49334741-49334741	p.I46I	1
chr12:49332815-49332815	p.Y154F	1

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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=2

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	1								1	1		1		1			1			5
# mutation	1								1	1		2		1			1			6
nonsynonymous SNV									1	1		1								4
synonymous SNV	1											1		1			1			2

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
chr12:49333860	p.I46I	1
chr12:49334741	p.I42I	1
chr12:49334753	p.I33I	1
chr12:49334780	p.K15M	1
chr12:49332794	p.L12L	1
chr12:49334835	p.T161I	1
chr12:49333511	p.R104Q	1
chr12:49334843	p.R104R	1
chr12:49333512	p.R97L	1
chr12:49333532	p.R79G	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 ARF3 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 ARF3

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


ACVR1B,ARF3,ASB8,ATP6AP1,BAZ2A,COPZ1,DAZAP2, DCTN4,DNAJC14,FOXA1,LARP4,LOC144438,LRBA,MARVELD2, NECAP1,PRKAG1,RAB5B,RNF14,SPRYD3,SUOX,TMBIM6	ALDH18A1,ARF3,GID8,CANT1,CDH1,DLG3,FAM102A, FAM83H,GOLM1,HDAC1,HHAT,ILDR1,MAPK13,MARVELD2, PDIA3,PDIA3P1,PIP4K2C,RAB11FIP4,SEC23B,SLC35A2,TM9SF1

ARF3,ASB8,ATP5B,ATG101,COPZ1,CS,DAZAP2, DDX23,DNAJC14,LARP4,LLPH,MFSD5,PIP4K2C,PRR13, RAB35,RAB5B,SENP1,SCAF11,SPRYD3,SUDS3,TMBIM6	ACOX1,ALAS1,AMBRA1,ARF3,BSG,CAPN2,CDH1, CEACAM5,CEACAM7,RHOV___CHP1,ABHD17C,FUT3,GBA,GBAP1, MGLL,OPN3,PAPSS2,PPARG,SFXN1,SH3KBP1,ZNF217

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 ARF3

There's no related Drug.

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Cross referenced IDs for ARF3

* 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