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 ARF1

Basic gene info.	Gene symbol	ARF1
	Gene name	ADP-ribosylation factor 1
	Synonyms	-
	Cytomap	UCSC genome browser: 1q42
	Genomic location	chr1 :228270360-228286913
	Type of gene	protein-coding
	RefGenes	NM_001024226.1, NM_001024227.1,NM_001024228.1,NM_001658.3,
	Ensembl id	ENSG00000143761
	Description	-
	Modification date	20141207
dbXrefs	MIM : 103180
	HGNC : HGNC
	Ensembl : ENSG00000143761
	HPRD : 00054
	Vega : OTTHUMG00000037595
Protein	UniProt: P84077 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARF1
	BioGPS: 375
	Gene Expression Atlas: ENSG00000143761
	The Human Protein Atlas: ENSG00000143761
Pathway	NCI Pathway Interaction Database: ARF1
	KEGG: ARF1
	REACTOME: ARF1
	ConsensusPathDB
	Pathway Commons: ARF1
Metabolism	MetaCyc: ARF1
	HUMANCyc: ARF1
Regulation	Ensembl's Regulation: ENSG00000143761
	miRBase: chr1 :228,270,360-228,286,913
	TargetScan: NM_001024226
	cisRED: ENSG00000143761
Context	iHOP: ARF1
	cancer metabolism search in PubMed: ARF1
	UCL Cancer Institute: ARF1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ARF1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	103180; gene.
Orphanet
Disease	KEGG Disease: ARF1
	MedGen: ARF1 (Human Medical Genetics with Condition)
	ClinVar: ARF1
Phenotype	MGI: ARF1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ARF1	chr1	228285215	228285235		chr1	228324711	228324731

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 ARF1 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
DA131615	GUK1	1	65	1	228328003	228328067	ARF1	62	629	1	228284778	228285698
BQ183357	ARF1	19	512	1	228286417	228286910	PLCD4	510	690	2	219500615	219501106
AV749342	PDIA3	1	226	15	44061720	44062741	ARF1	223	484	1	228286648	228286910
BG272060	ATXN7	44	183	3	63988882	63989021	ARF1	179	244	1	228286285	228286350
W94280	DCAF5	15	316	14	69518853	69519154	ARF1	306	481	1	228286629	228286803
AL041701	ARF1	19	86	1	228286375	228286442	ARF1	77	526	1	228286002	228286451
W94277	ARF1	10	291	1	228286629	228286910	DCAF5	281	469	14	69518853	69519041
BF809756	CTCF	11	333	16	67617758	67618080	ARF1	326	380	1	228284855	228284909
BF893864	ARF1	1	79	1	228285722	228285802	ARF1	79	314	1	228285789	228286024
M62013	ARF1	1	76	1	228286602	228286677	PFN2	75	304	3	149683697	149683926

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=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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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
chr1:228285575-228285575	p.A136V	3
chr1:228284827-228284827	p.I4I	2
chr1:228285621-228285621	p.R151R	2
chr1:228285654-228285654	p.S162S	2
chr1:228285694-228285694	p.Q176E	2
chr1:228285583-228285583	p.I139V	1
chr1:228285076-228285076	p.I61S	1
chr1:228285584-228285584	p.I139T	1
chr1:228284857-228284858	p.E17fs*22	1
chr1:228285130-228285130	p.R79H	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					2		1	1	3				2	3		4
# mutation		1		1					2		1	1	4				2	4		4
nonsynonymous SNV		1							1			1	1					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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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
chr1:228284827	p.I4M,ARF1	2
chr1:228285654	p.S162S,ARF1	2
chr1:228285355	p.I139T,ARF1	1
chr1:228285383	p.R149H,ARF1	1
chr1:228284846	p.R151R,ARF1	1
chr1:228285396	p.G11S,ARF1	1
chr1:228284888	p.T161T,ARF1	1
chr1:228285405	p.L25M,ARF1	1
chr1:228284922	p.K36T,ARF1	1
chr1:228285584	p.E168E,ARF1	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 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

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


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

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 ARF1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P84077; -.
Chemistry	ChEMBL	CHEMBL5985; -.
Organism-specific databases	PharmGKB	PA24934; -.
Organism-specific databases	CTD	375; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB02774	ADP-ribosylation factor 1	experimental	1,3-Propandiol
DB04077	ADP-ribosylation factor 1	experimental	Glycerol
DB04121	ADP-ribosylation factor 1	experimental	Guanosine-3'-Monophosphate-5'-Diphosphate
DB04137	ADP-ribosylation factor 1	experimental	Guanosine-5'-Triphosphate
DB04315	ADP-ribosylation factor 1	experimental	Guanosine-5'-Diphosphate
DB07348	ADP-ribosylation factor 1	experimental	1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE
DB08231	ADP-ribosylation factor 1	experimental	MYRISTIC ACID
DB00122	ADP-ribosylation factor 1	approved; nutraceutical	Choline

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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