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 PAICS
Basic gene info.Gene symbolPAICS
Gene namephosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase
SynonymsADE2|ADE2H1|AIRC|PAIS
CytomapUCSC genome browser: 4q12
Genomic locationchr4 :57302268-57327534
Type of geneprotein-coding
RefGenesNM_001079524.1,
NM_001079525.1,NM_006452.3,
Ensembl idENSG00000128050
DescriptionAIR carboxylaseSAICAR synthetasemultifunctional protein ADE2multifunctional protein ADE2H1
Modification date20141207
dbXrefs MIM : 172439
HGNC : HGNC
Ensembl : ENSG00000128050
HPRD : 01401
Vega : OTTHUMG00000160957
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAICS
BioGPS: 10606
Gene Expression Atlas: ENSG00000128050
The Human Protein Atlas: ENSG00000128050
PathwayNCI Pathway Interaction Database: PAICS
KEGG: PAICS
REACTOME: PAICS
ConsensusPathDB
Pathway Commons: PAICS
MetabolismMetaCyc: PAICS
HUMANCyc: PAICS
RegulationEnsembl's Regulation: ENSG00000128050
miRBase: chr4 :57,302,268-57,327,534
TargetScan: NM_001079524
cisRED: ENSG00000128050
ContextiHOP: PAICS
cancer metabolism search in PubMed: PAICS
UCL Cancer Institute: PAICS
Assigned class in ccmGDBC

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

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

Mutations for PAICS
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PAICS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DC389672CENPC1142246840555668411262PAICS41960645732553657325723

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)        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)

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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=28)
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
chr4:57307916-57307916p.S61F2
chr4:57314967-57314967p.R248Q2
chr4:57318195-57318195p.L336Q2
chr4:57314612-57314612p.S167C1
chr4:57318064-57318064p.C292*1
chr4:57302459-57302459p.A20D1
chr4:57319885-57319885p.W383G1
chr4:57314659-57314659p.I183L1
chr4:57318118-57318118p.I310I1
chr4:57307824-57307824p.?1

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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
# sample 2 4    2  1    3  2
# mutation 2 4    2  1    3  2
nonsynonymous SNV 1 3    2  1    1  2
synonymous SNV 1 1            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])

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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
chr4:57318153p.E23K,PAICS1
chr4:57307879p.L109F,PAICS1
chr4:57318164p.I172V,PAICS1
chr4:57312971p.I175M,PAICS1
chr4:57319885p.L176L,PAICS1
chr4:57314704p.D197H,PAICS1
chr4:57325560p.R222Q,PAICS1
chr4:57314715p.I284I,PAICS1
chr4:57325593p.I293V,PAICS1
chr4:57314718p.P294P,PAICS1

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 PAICS 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 PAICS

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

ABCE1,NOA1,CCNA2,CENPE,DCUN1D4,FIP1L1,KIF18A,
MAD2L1,NAA15,NCAPG,NCAPH,NEIL3,PAICS,PLK4,
POLR2B,PPAT,SCFD2,SGOL1,SRP72,TTK,WDR12
FAXC,CTBP2,DKC1,DSC2,E2F5,ESRP1,FAM60A,
HDAC2,LRRC8D,METAP1,NKRF,OAT,PAICS,PPAT,
SET,SMARCC1,SRPK1,SSX2IP,TDP1,TTC19,UCK2

CDC45,CHEK2,ENOPH1,GRPEL1,GRSF1,H2AFZ,HSPD1,
DANCR,LYAR,MND1,MRTO4,NCAPG,PA2G4,PAICS,
PPAT,RANBP1,RCC1,SLBP,SPAG5,SRP72,TRIP13
CCT6A,CDC25A,DKC1,DNAJC9,ECT2,EXO1,FARSB,
HSPD1,KIAA0020,MCM4,MCM6,NOP14,ORC6,PA2G4P4,
PAICS,RCC1,RUVBL1,SUV39H2,NDC1,WDR4,ZWILCH
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 PAICS
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
DB00128phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetaseapproved; nutraceuticalL-Aspartic Acid
DB00145phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetaseapproved; nutraceuticalGlycine
DB00130phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetaseapproved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for PAICS
* 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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