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 ADSS
Basic gene info.Gene symbolADSS
Gene nameadenylosuccinate synthase
SynonymsADEH|ADSS 2
CytomapUCSC genome browser: 1q44
Genomic locationchr1 :244571793-244615436
Type of geneprotein-coding
RefGenesNM_001126.3,
Ensembl idENSG00000035687
DescriptionAMPSase 2IMP--aspartate ligase 2L-type adenylosuccinate synthetaseadSS 2adenylosuccinate synthetase (Ade(-)H-complementing)adenylosuccinate synthetase isozyme 2adenylosuccinate synthetase, acidic isozymeadenylosuccinate synthetase, liver isozyme
Modification date20141207
dbXrefs MIM : 103060
HGNC : HGNC
Ensembl : ENSG00000035687
HPRD : 00050
Vega : OTTHUMG00000040102
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADSS
BioGPS: 159
Gene Expression Atlas: ENSG00000035687
The Human Protein Atlas: ENSG00000035687
PathwayNCI Pathway Interaction Database: ADSS
KEGG: ADSS
REACTOME: ADSS
ConsensusPathDB
Pathway Commons: ADSS
MetabolismMetaCyc: ADSS
HUMANCyc: ADSS
RegulationEnsembl's Regulation: ENSG00000035687
miRBase: chr1 :244,571,793-244,615,436
TargetScan: NM_001126
cisRED: ENSG00000035687
ContextiHOP: ADSS
cancer metabolism search in PubMed: ADSS
UCL Cancer Institute: ADSS
Assigned class in ccmGDBC

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Phenotypic Information for ADSS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADSS
Familial Cancer Database: ADSS
* 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_PURINE_METABOLISM
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ADSS
MedGen: ADSS (Human Medical Genetics with Condition)
ClinVar: ADSS
PhenotypeMGI: ADSS (International Mouse Phenotyping Consortium)
PhenomicDB: ADSS

Mutations for ADSS
* 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
ovaryADSSchr1244595881244596081ADSSchr1244598415244598615
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 ADSS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB348377ADSS14681244572154244572621JMJD1C465537106497600764976078

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 # sample          1      
GAIN (# sample)                 
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=6

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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=17)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr1:244587341-244587341p.G165G5
chr1:244574619-244574619p.R430*4
chr1:244587324-244587324p.S171L3
chr1:244579341-244579341p.T370T2
chr1:244582125-244582125p.Y294Y2
chr1:244580947-244580947p.M351I2
chr1:244583488-244583488p.L258L2
chr1:244587358-244587358p.G160S1
chr1:244614960-244614960p.A54T1
chr1:244583581-244583581p.K228fs*41

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  11  2    313  2318
# mutation2  8  2    313  2418
nonsynonymous SNV2  6  2    211  14 4
synonymous SNV   2       1 2  1 14
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
chr1:244587341p.G165G5
chr1:244579368p.Q288E1
chr1:244586155p.F94L1
chr1:244614960p.G278D1
chr1:244579370p.A54T1
chr1:244587290p.V276D1
chr1:244614999p.E41K1
chr1:244580948p.R430Q1
chr1:244587324p.I249I1
chr1:244574618p.A9V1

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 ADSS 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 ADSS

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

ADSSL1,AK1,AKT1,BRF1,BTBD6,CCDC85C,CINP,
CRIP2,GSTZ1,INF2,CEP170B,KLC1,MTA1,PACS2,
PAK4,PWRN2,SIVA1,WBP1,WDR25,ZBTB42,ZFYVE21
ADSSL1,MLIP,C8orf22,CA3,CKMT2,CORO6,ENAM,
FBXO40,HRC,KLHL33,MYH1,MYOM1,PDE4DIP,PGAM2,
PYGM,SLC25A34,SLC25A4,SYPL2,TMEM52,TNNT3,TRIM7

ADSSL1,ALPPL2,BEX1,MRGPRG-AS1,LAMP5,C3orf35,FAM218A,
CMAHP,CNTFR,FGF3,KCP,LOC100131551,MAEL,MAGED4,
NTF4,OOSP2,SACS,SCN2A,SPANXN2,SUMO1P1,TM9SF1
AATK,ABCA4,ADSSL1,AGAP11,ALDH3B1,ALS2,AQP3,
B3GALT2,MB21D2,MLXIPL,MPP6,PLLP,PNLIPRP2,RHBDL1,
RNF141,SIRPA,SLC6A6,TEKT3,UNC93A,UPK3A,VNN1
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 ADSS
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
DB02109adenylosuccinate synthaseexperimentalHadacidin
DB02493adenylosuccinate synthaseexperimentalHydantocidin-5'-Phosphate
DB02666adenylosuccinate synthaseexperimental(C8-R)-Hydantocidin 5'-Phosphate
DB02682adenylosuccinate synthaseexperimental2-Deamino-6-Deoxy-6thiophosphite-5'-Phosphate Guanosine
DB02836adenylosuccinate synthaseexperimentalGuanosine 5'-Diphosphate 2':3'-Cyclic Monophosphate
DB02954adenylosuccinate synthaseexperimental(Carboxyhydroxyamino)Ethanoic Acid
DB03146adenylosuccinate synthaseexperimental2-Deazo-6-Thiophosphate Guanosine-5'-Monophosphate
DB04315adenylosuccinate synthaseexperimentalGuanosine-5'-Diphosphate
DB04460adenylosuccinate synthaseexperimental(C8-S)-Hydantocidin 5'-Phosphate
DB04566adenylosuccinate synthaseexperimentalInosinic Acid
DB04160adenylosuccinate synthaseexperimentalDiphosphate
DB00128adenylosuccinate synthaseapproved; nutraceuticalL-Aspartic Acid
DB03510adenylosuccinate synthaseexperimental6-O-Phosphoryl Inosine Monophosphate
DB02580adenylosuccinate synthaseexperimental1-(2-Methoxy-Ethoxy)-2-{2-[2-(2-Methoxy-Ethoxy]-Ethoxy}-Ethane
DB00864adenylosuccinate synthaseapproved; investigationalTacrolimus


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Cross referenced IDs for ADSS
* 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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