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 ARF1
Basic gene info.Gene symbolARF1
Gene nameADP-ribosylation factor 1
Synonyms-
CytomapUCSC genome browser: 1q42
Genomic locationchr1 :228270360-228286913
Type of geneprotein-coding
RefGenesNM_001024226.1,
NM_001024227.1,NM_001024228.1,NM_001658.3,
Ensembl idENSG00000143761
Description-
Modification date20141207
dbXrefs MIM : 103180
HGNC : HGNC
Ensembl : ENSG00000143761
HPRD : 00054
Vega : OTTHUMG00000037595
ProteinUniProt: P84077
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARF1
BioGPS: 375
Gene Expression Atlas: ENSG00000143761
The Human Protein Atlas: ENSG00000143761
PathwayNCI Pathway Interaction Database: ARF1
KEGG: ARF1
REACTOME: ARF1
ConsensusPathDB
Pathway Commons: ARF1
MetabolismMetaCyc: ARF1
HUMANCyc: ARF1
RegulationEnsembl's Regulation: ENSG00000143761
miRBase: chr1 :228,270,360-228,286,913
TargetScan: NM_001024226
cisRED: ENSG00000143761
ContextiHOP: ARF1
cancer metabolism search in PubMed: ARF1
UCL Cancer Institute: ARF1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ARF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ARF1
Familial Cancer Database: ARF1
* 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 103180; gene.
Orphanet
DiseaseKEGG Disease: ARF1
MedGen: ARF1 (Human Medical Genetics with Condition)
ClinVar: ARF1
PhenotypeMGI: ARF1 (International Mouse Phenotyping Consortium)
PhenomicDB: ARF1

Mutations for ARF1
* 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
There's no inter-chromosomal structural variation.
- 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
pancreasARF1chr1228285215228285235chr1228324711228324731
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 ARF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA131615GUK11651228328003228328067ARF1626291228284778228285698
BQ183357ARF1195121228286417228286910PLCD45106902219500615219501106
AV749342PDIA31226154406172044062741ARF12234841228286648228286910
BG272060ATXN74418336398888263989021ARF11792441228286285228286350
W94280DCAF515316146951885369519154ARF13064811228286629228286803
AL041701ARF119861228286375228286442ARF1775261228286002228286451
W94277ARF1102911228286629228286910DCAF5281469146951885369519041
BF809756CTCF11333166761775867618080ARF13263801228284855228284909
BF893864ARF11791228285722228285802ARF1793141228285789228286024
M62013ARF11761228286602228286677PFN2753043149683697149683926

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=17)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr1:228285575-228285575p.A136V3
chr1:228284827-228284827p.I4I2
chr1:228285621-228285621p.R151R2
chr1:228285654-228285654p.S162S2
chr1:228285694-228285694p.Q176E2
chr1:228285050-228285050p.N52N1
chr1:228285405-228285405p.A125T1
chr1:228285059-228285059p.T55T1
chr1:228284826-228284826p.I4S1
chr1:228285075-228285075p.I61L1

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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
# sample 1 1    2 113   23 4
# mutation 1 1    2 114   24 4
nonsynonymous SNV 1      1  11    4 3
synonymous SNV   1    1 1 3   2  1
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
chr1:228284827p.I4M,ARF12
chr1:228285654p.S162S,ARF12
chr1:228285343p.L122L,ARF11
chr1:228285355p.A125T,ARF11
chr1:228285383p.I139T,ARF11
chr1:228284846p.R149H,ARF11
chr1:228285396p.R151R,ARF11
chr1:228284888p.G11S,ARF11
chr1:228285405p.T161T,ARF11
chr1:228284922p.L25M,ARF11

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 ARF1 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 ARF1

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

ARF1,ARL8A,C1orf131,COA6,C1orf35,GUK1,H3F3A,
HAX1,JMJD4,JTB,KRTCAP2,MRPL55,PFDN2,PSMB4,
PYCR2,RNF187,SF3B4,SNAP47,SSR2,TMEM9,TRIM11
APOA1BP,ARF1,ATP6V0B,CHMP1A,COPE,GNB2,GPAA1,
JMJD8,LMAN2,PPP4C,RAB1B,RALY,RHOC,RNF187,
SLC25A39,SSSCA1,SYNGR2,TMEM205,TMEM208,TMEM222,YIPF3

ADIPOR1,APH1A,ARF1,B4GALT3,DEDD,HAX1,JTB,
KRTCAP2,MRPL24,MRPL55,MTX1,PMVK,PRCC,RAB25,
RNF187,RNPEP,LAMTOR2,SCAMP3,SSR2,TPM3,TRIM11
AP2S1,ARF1,ARPC1A,AURKAIP1,CIB1,COPE,EIF6,
GALE,GNG5,LMAN2,MED8,MPDU1,OSTF1,OTUB1,
PPP1CA,PPP4C,PSMD3,RAB1B,RER1,TALDO1,TMEM208
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 ARF1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P84077; -.
ChemistryChEMBL CHEMBL5985; -.
Organism-specific databasesPharmGKB PA24934; -.
Organism-specific databasesCTD 375; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02774ADP-ribosylation factor 1experimental1,3-Propandiol
DB04077ADP-ribosylation factor 1experimentalGlycerol
DB04121ADP-ribosylation factor 1experimentalGuanosine-3'-Monophosphate-5'-Diphosphate
DB04137ADP-ribosylation factor 1experimentalGuanosine-5'-Triphosphate
DB04315ADP-ribosylation factor 1experimentalGuanosine-5'-Diphosphate
DB07348ADP-ribosylation factor 1experimental1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE
DB08231ADP-ribosylation factor 1experimentalMYRISTIC ACID
DB00122ADP-ribosylation factor 1approved; nutraceuticalCholine


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Cross referenced IDs for ARF1
* 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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