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 ARF3
Basic gene info.Gene symbolARF3
Gene nameADP-ribosylation factor 3
Synonyms-
CytomapUCSC genome browser: 12q13
Genomic locationchr12 :49329991-49351252
Type of geneprotein-coding
RefGenesNM_001659.2,
Ensembl idENSG00000134287
Descriptionsmall GTP binding protein
Modification date20141207
dbXrefs MIM : 103190
HGNC : HGNC
Ensembl : ENSG00000134287
HPRD : 00056
Vega : OTTHUMG00000168080
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARF3
BioGPS: 377
Gene Expression Atlas: ENSG00000134287
The Human Protein Atlas: ENSG00000134287
PathwayNCI Pathway Interaction Database: ARF3
KEGG: ARF3
REACTOME: ARF3
ConsensusPathDB
Pathway Commons: ARF3
MetabolismMetaCyc: ARF3
HUMANCyc: ARF3
RegulationEnsembl's Regulation: ENSG00000134287
miRBase: chr12 :49,329,991-49,351,252
TargetScan: NM_001659
cisRED: ENSG00000134287
ContextiHOP: ARF3
cancer metabolism search in PubMed: ARF3
UCL Cancer Institute: ARF3
Assigned class in ccmGDBC

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Phenotypic Information for ARF3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ARF3
MedGen: ARF3 (Human Medical Genetics with Condition)
ClinVar: ARF3
PhenotypeMGI: ARF3 (International Mouse Phenotyping Consortium)
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.

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 ARF3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
H14073GBF118410104142570104142653ARF376407124933208349332407
BF509886RAD23A17192191306428113064456ARF3188434124933193149332177
BQ668805ARF3159124933079349330851NDUFA660458224248211842486691
R23430ARF34183124933257449332754OGFOD217522512123463043123463093
BG001600ARF31268124933270449333517SLC38A7258337165870063358700712
AA527815ARF31289124933160449331892ARF3284346124933151449331576
AI742354ARF3171124933131949331389ARF358342124933151849331802
R85158GBF118410104142570104142653ARF376276124933208349332284
AA525008ARF31289124933160449331892ARF3284368124933151449331598
BC020999CCNB1IP113862828142077952920797531ARF328293851124933248949351235
H38464GBF118410104142570104142653ARF376350124933208349332356
BQ331543ARF322240124933378249334840ITPR2234508122695967626959951

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

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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=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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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
chr12:49333815-49333815p.R75Q3
chr12:49332794-49332794p.T161I1
chr12:49334741-49334741p.I46I1
chr12:49332815-49332815p.Y154F1
chr12:49334753-49334753p.I42I1
chr12:49333501-49333501p.L107L1
chr12:49334777-49334777p.L34L1
chr12:49333511-49333511p.R104Q1
chr12:49334835-49334835p.K15M1
chr12:49333512-49333512p.R104W1

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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
# sample1       11 1 1  1  5
# mutation1       11 2 1  1  6
nonsynonymous SNV        11 1       4
synonymous SNV1          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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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
chr12:49333511p.R104Q1
chr12:49334843p.R104R1
chr12:49333512p.R97L1
chr12:49333532p.R79G1
chr12:49333804p.K73K1
chr12:49333820p.G69R1
chr12:49333834p.N60S1
chr12:49333860p.I46I1
chr12:49334741p.I42I1
chr12:49334753p.I33I1

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 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

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

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
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 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



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