Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 ASL
Basic gene info.Gene symbolASL
Gene nameargininosuccinate lyase
SynonymsASAL
CytomapUCSC genome browser: 7q11.21
Genomic locationchr7 :65540833-65558329
Type of geneprotein-coding
RefGenesNM_000048.3,
NM_001024943.1,NM_001024944.1,NM_001024946.1,
Ensembl idENSG00000126522
Descriptionargininosuccinasearginosuccinase
Modification date20141219
dbXrefs MIM : 608310
HGNC : HGNC
Ensembl : ENSG00000126522
HPRD : 01948
Vega : OTTHUMG00000022876
ProteinUniProt: P04424
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ASL
BioGPS: 435
Gene Expression Atlas: ENSG00000126522
The Human Protein Atlas: ENSG00000126522
PathwayNCI Pathway Interaction Database: ASL
KEGG: ASL
REACTOME: ASL
ConsensusPathDB
Pathway Commons: ASL
MetabolismMetaCyc: ASL
HUMANCyc: ASL
RegulationEnsembl's Regulation: ENSG00000126522
miRBase: chr7 :65,540,833-65,558,329
TargetScan: NM_000048
cisRED: ENSG00000126522
ContextiHOP: ASL
cancer metabolism search in PubMed: ASL
UCL Cancer Institute: ASL
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 207900; phenotype.
608310; gene.
Orphanet 23; Argininosuccinic aciduria.
DiseaseKEGG Disease: ASL
MedGen: ASL (Human Medical Genetics with Condition)
ClinVar: ASL
PhenotypeMGI: ASL (International Mouse Phenotyping Consortium)
PhenomicDB: ASL

Mutations for ASL
* 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
pancreasASLchr76555021865550238chr76549660065496620
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 ASL related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF853820ASL1642776554883665549245DIAPH14255295140954574140954678

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr7:65553815-65553815p.S247L2
chr7:65554649-65554649p.L343L2
chr7:65553914-65553914p.?2
chr7:65546942-65546942p.L55L2
chr7:65557836-65557836p.A444A1
chr7:65552756-65552756p.A232A1
chr7:65547366-65547366p.E73D1
chr7:65554635-65554635p.M339V1
chr7:65551587-65551587p.L154L1
chr7:65557572-65557572p.S391Y1

Top
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
# sample35 31   2  632  97 5
# mutation35 31   2  632  106 5
nonsynonymous SNV24 3    2  43   66 3
synonymous SNV11  1      2 2  4  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])

Top
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
chr7:65553815p.L55L,ASL2
chr7:65553885p.S221L,ASL2
chr7:65546942p.A384T,ASL2
chr7:65557610p.F244F,ASL2
chr7:65554646p.E148Q,ASL1
chr7:65548112p.T318N,ASL1
chr7:65557802p.L154F,ASL1
chr7:65552730p.M319V,ASL1
chr7:65554649p.L154L,ASL1
chr7:65548151p.V322V,ASL1

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 ASL 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]

Top
Gene Expression for ASL

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ABCB8,ALKBH7,ASL,TSR3,C7orf50,LAMTOR4,CHCHD5,
DDRGK1,FASTK,FBXL15,FIS1,JOSD2,LMAN2,NAGLU,
NDUFS7,NUDT22,RABAC1,SDSL,SIL1,STUB1,TMUB1
AAMP,ASL,ASMTL,ASPSCR1,BRMS1,OXLD1,CORO1B,
CRELD2,DDRGK1,DGCR6L,GSDMD,LMAN2,NT5C,PEX11G,
PEX16,PIGQ,PNKP,PRPF31,SELO,TEX264,TMEM141

ADCK2,AP1S1,ARPC1A,ASL,ATP5J2,BCL7B,LAMTOR4,
CHCHD2,CRCP,DDC,DNAJC30,FIS1,GNB2,HDHD3,
MDH2,NDUFB2,SLC25A13,TBRG4,TMEM120A,TP53TG1,ZNHIT1
ARPC4,ASL,AURKAIP1,BRMS1,AP5S1,CYB561D2,DHRS7B,
GNG5,HMOX2,HN1,LMAN2,MPDU1,MRPS11,NDUFA9,
PPP1CA,SDSL,SLC25A39,TALDO1,TPI1,UQCRC1,VPS25
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for ASL
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA25046; -.
Organism-specific databasesCTD 435; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125argininosuccinate lyaseapproved; nutraceuticalL-Arginine
DB02267argininosuccinate lyaseexperimentalArgininosuccinate
DB03814argininosuccinate lyaseexperimental2-(N-Morpholino)-Ethanesulfonic Acid
DB03904argininosuccinate lyaseexperimentalUrea


Top
Cross referenced IDs for ASL
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas