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 ARG1
Basic gene info.Gene symbolARG1
Gene namearginase 1
Synonyms-
CytomapUCSC genome browser: 6q23
Genomic locationchr6 :131894343-131905472
Type of geneprotein-coding
RefGenesNM_000045.3,
NM_001244438.1,
Ensembl idENSG00000118520
Descriptionarginase, liverarginase-1liver-type arginasetype I arginase
Modification date20141219
dbXrefs MIM : 608313
HGNC : HGNC
Ensembl : ENSG00000118520
HPRD : 01947
Vega : OTTHUMG00000015566
ProteinUniProt: P05089
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARG1
BioGPS: 383
Gene Expression Atlas: ENSG00000118520
The Human Protein Atlas: ENSG00000118520
PathwayNCI Pathway Interaction Database: ARG1
KEGG: ARG1
REACTOME: ARG1
ConsensusPathDB
Pathway Commons: ARG1
MetabolismMetaCyc: ARG1
HUMANCyc: ARG1
RegulationEnsembl's Regulation: ENSG00000118520
miRBase: chr6 :131,894,343-131,905,472
TargetScan: NM_000045
cisRED: ENSG00000118520
ContextiHOP: ARG1
cancer metabolism search in PubMed: ARG1
UCL Cancer Institute: ARG1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ARG1 in cancer cell metabolism1. Stenmark KR, Tuder RM, El Kasmi KC (2015) Metabolic Reprogramming and Inflammation Act in Concert to Control Vascular Remodeling in Hypoxic Pulmonary Hypertension. J Appl Physiol (1985): jap 00283 02015. doi: 10.1152/japplphysiol.00283.2015. go to article

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Phenotypic Information for ARG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ARG1
Familial Cancer Database: ARG1
* 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
KEGG_ARGININE_AND_PROLINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 207800; phenotype.
608313; gene.
Orphanet 90; Argininemia.
DiseaseKEGG Disease: ARG1
MedGen: ARG1 (Human Medical Genetics with Condition)
ClinVar: ARG1
PhenotypeMGI: ARG1 (International Mouse Phenotyping Consortium)
PhenomicDB: ARG1

Mutations for ARG1
* 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
ovaryARG1chr6131904653131904673MED23chr6131906140131906160
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 ARG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
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
chr6:131897818-131897818p.E25K2
chr6:131894467-131894467p.F15L2
chr6:131904603-131904603p.L258L2
chr6:131904251-131904251p.D204E2
chr6:131897815-131897815p.V24L2
chr6:131902413-131902413p.V120V2
chr6:131904971-131904971p.A298S1
chr6:131902478-131902478p.G142E1
chr6:131904271-131904271p.V211G1
chr6:131900254-131900254p.C45Y1

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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 2 3        31  22 4
# mutation 2 3        31  22 5
nonsynonymous SNV 2 2        21  12 4
synonymous SNV   1        1   1  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
chr6:131897815p.V24L,ARG12
chr6:131903781p.G235R,ARG11
chr6:131903792p.G257S,ARG11
chr6:131904242p.G283G,ARG11
chr6:131894434p.T290T,ARG11
chr6:131904498p.K4K,ARG11
chr6:131897803p.T292I,ARG11
chr6:131904532p.P20S,ARG11
chr6:131897807p.G305R,ARG11
chr6:131904598p.R21Q,ARG11

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 ARG1 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 ARG1

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

APCS,APOA2,APOA4,APOB,APOC3,ARG1,C8A,
C9,CREB3L3,CRP,F2,FABP1,FGF23,GDF2,
HP,ITIH1,MT1B,PLG,SERPINA7,SLC17A2,TM4SF5
ALMS1,ANKRD36,ARG1,CCDC38,CDCA7,CENPJ,CCP110,
FLJ10213,HIST3H3,INPP5F,INTS8,MC2R,RBBP6,SCML2,
SHPRH,SNX18,USP17L6P,XPO1,XRCC2,ZBTB10,ZNF318

AJAP1,ARG1,AVPR1A,CCDC155,CLEC4D,CXCR1,CXCR2,
SUPT20HL2,FPR1,FPR2,HRH2,IL7R,LINGO4,MGAM,
OPN5,PADI4,PGLYRP1,S100A12,SELE,TCTE1,TNC
SLC35G3,ARG1,BEND2,LINC00305,CMTM2,CXCR2,FAM74A4,
GAGE10,LRIT1,NXF4,OR52E2,OR52E6,PADI4,PLCZ1,
SELE,SLC22A24,SPRR2G,SSX5,STRA8,TREML4,ZNF735
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 ARG1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P05089; -.
ChemistryChEMBL CHEMBL1075097; -.
Organism-specific databasesPharmGKB PA24947; -.
Organism-specific databasesCTD 383; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00129arginase, liverapproved; nutraceuticalL-Ornithine
DB01983arginase, liverexperimental2(S)-Amino-6-Boronohexanoic Acid
DB02381arginase, liverexperimentalNor-N-Omega-Hydroxy-L-Arginine
DB02499arginase, liverexperimentalDinor-N(Omega)-Hydroxy-L-Arginine
DB02689arginase, liverexperimentalS-{2-[Amino(Dihydroxy)-Lambda~4~-Sulfanyl]Ethyl}-D-Cysteine
DB03144arginase, liverexperimentalN-Omega-Hydroxy-L-Arginine
DB03731arginase, liverexperimentalS-2-(Boronoethyl)-L-Cysteine
DB03904arginase, liverexperimentalUrea
DB04197arginase, liverexperimentalDescarboxy-nor-N(Omega)-Hydroxy-L-Arginine
DB04530arginase, liverexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB04585arginase, liverexperimentalDEHYDRO-2(S)-AMINO-6-BORONOHEXANOIC ACID
DB04648arginase, liverexperimentalS-propylamine-L-cysteine
DB01222arginase, liverapproved; investigationalBudesonide
DB00588arginase, liverapproved; investigationalFluticasone Propionate
DB00716arginase, liverapprovedNedocromil
DB01001arginase, liverapprovedSalbutamol
DB00125arginase, liverapproved; nutraceuticalL-Arginine


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Cross referenced IDs for ARG1
* 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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