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 ASS1
Basic gene info.Gene symbolASS1
Gene nameargininosuccinate synthase 1
SynonymsASS|CTLN1
CytomapUCSC genome browser: 9q34.1
Genomic locationchr9 :133320093-133376661
Type of geneprotein-coding
RefGenesNM_000050.4,
NM_054012.3,
Ensembl idENSG00000130707
Descriptionargininosuccinate synthaseargininosuccinate synthetase 1citrulline--aspartate ligasecitrulline-aspartate ligase
Modification date20141222
dbXrefs MIM : 603470
HGNC : HGNC
Ensembl : ENSG00000130707
HPRD : 04590
Vega : OTTHUMG00000020806
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ASS1
BioGPS: 445
Gene Expression Atlas: ENSG00000130707
The Human Protein Atlas: ENSG00000130707
PathwayNCI Pathway Interaction Database: ASS1
KEGG: ASS1
REACTOME: ASS1
ConsensusPathDB
Pathway Commons: ASS1
MetabolismMetaCyc: ASS1
HUMANCyc: ASS1
RegulationEnsembl's Regulation: ENSG00000130707
miRBase: chr9 :133,320,093-133,376,661
TargetScan: NM_000050
cisRED: ENSG00000130707
ContextiHOP: ASS1
cancer metabolism search in PubMed: ASS1
UCL Cancer Institute: ASS1
Assigned class in ccmGDBC

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Phenotypic Information for ASS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ASS1
Familial Cancer Database: ASS1
* 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
Orphanet
DiseaseKEGG Disease: ASS1
MedGen: ASS1 (Human Medical Genetics with Condition)
ClinVar: ASS1
PhenotypeMGI: ASS1 (International Mouse Phenotyping Consortium)
PhenomicDB: ASS1

Mutations for ASS1
* 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
ovaryASS1chr9133346886133346906ASS1chr9133329317133329337
pancreasASS1chr9133370913133370933ASS1chr9133373445133373465
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 ASS1 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1       1        
GAIN (# sample)1                
LOSS (# sample)        1        
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)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=28)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr9:133333965-133333965p.A118T4
chr9:133364742-133364742p.G287G2
chr9:133355773-133355773p.G259S2
chr9:133339508-133339508p.Q125R1
chr9:133346888-133346888p.L195L1
chr9:133370305-133370305p.S341F1
chr9:133333847-133333847p.Q78Q1
chr9:133339513-133339513p.R127W1
chr9:133364772-133364772p.I297I1
chr9:133370310-133370310p.E343K1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31152 1 4  4 1  118 5
# mutation31152 1 4  4 1  138 6
nonsynonymous SNV21131 1 2  4 1  78 2
synonymous SNV1  21   2       6  4
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
chr9:133342131p.D30N,ASS11
chr9:133355773p.R146K,ASS11
chr9:133333871p.G275E,ASS11
chr9:133364801p.K412T,ASS11
chr9:133342148p.F44F,ASS11
chr9:133355784p.M147T,ASS11
chr9:133333923p.S278T,ASS11
chr9:133364826p.V64F,ASS11
chr9:133342180p.R153W,ASS11
chr9:133355792p.R279P,ASS11

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 ASS1 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 ASS1

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

AK2,ASS1,BID,SMCO4,USB1,C1orf106,CARD9,
CDC42EP1,CEBPB,CSTB,ECE2,TLDC1,PDXK,PDZK1IP1,
PFKP,PGM1,POR,PSMB2,SH2B2,SLC35C1,STEAP3
ALDH1L1,ANKRD53,ASS1,C20orf27,APMAP,CALCRL,CIDEA,
ECHDC3,GLUL,GLYCTK,HEBP2,HRSP12,MLXIPL,MOCS1,
PC,PMM1,RASL10B,SHMT1,TM7SF2,TMEM100,TMEM120A

ASS1,GSKIP,CYSTM1,CASP10,CCL28,F2RL1,GTF2A2,
KCNK1,KDELR3,PDZK1IP1,PI3,RSPH1,S100A14,S100A16,
S100A6,SEMG1,SEMG2,SERPINB1,STS,SYT12,TC2N
ASS1,CARD16,CASP1,CASP5,CD274,CLEC6A,ETV7,
FAM26F,FCGR1C,GBP1,GRAMD2,IFI35,LOC400696,LYPD5,
NOS2,PARP9,PSMA3,PSMB2,PSME1,PSME2,WARS
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 ASS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125argininosuccinate synthase 1approved; nutraceuticalL-Arginine
DB00128argininosuccinate synthase 1approved; nutraceuticalL-Aspartic Acid
DB00155argininosuccinate synthase 1approved; nutraceuticalL-Citrulline
DB00171argininosuccinate synthase 1approved; nutraceuticalAdenosine triphosphate
DB02267argininosuccinate synthase 1experimentalArgininosuccinate
DB04395argininosuccinate synthase 1experimentalPhosphoaminophosphonic Acid-Adenylate Ester
DB00536argininosuccinate synthase 1approvedGuanidine
DB04077argininosuccinate synthase 1experimentalGlycerol
DB03904argininosuccinate synthase 1experimentalUrea


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Cross referenced IDs for ASS1
* 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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