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 ATIC
Basic gene info.Gene symbolATIC
Gene name5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
SynonymsAICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH
CytomapUCSC genome browser: 2q35
Genomic locationchr2 :216176678-216214496
Type of geneprotein-coding
RefGenesNM_004044.6,
Ensembl idENSG00000138363
Description5-aminoimidazole-4-carboxamide-1-beta-D-ribonucleotide transformylase/inosinicaseAICAR formyltransferase/IMP cyclohydrolase bifunctional enzymeAICARFT/IMPCHASEbifunctional purine biosynthesis protein PURHepididymis secretory sperm binding protein Li 7
Modification date20141207
dbXrefs MIM : 601731
HGNC : HGNC
Ensembl : ENSG00000138363
HPRD : 03434
Vega : OTTHUMG00000133023
ProteinUniProt: P31939
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ATIC
BioGPS: 471
Gene Expression Atlas: ENSG00000138363
The Human Protein Atlas: ENSG00000138363
PathwayNCI Pathway Interaction Database: ATIC
KEGG: ATIC
REACTOME: ATIC
ConsensusPathDB
Pathway Commons: ATIC
MetabolismMetaCyc: ATIC
HUMANCyc: ATIC
RegulationEnsembl's Regulation: ENSG00000138363
miRBase: chr2 :216,176,678-216,214,496
TargetScan: NM_004044
cisRED: ENSG00000138363
ContextiHOP: ATIC
cancer metabolism search in PubMed: ATIC
UCL Cancer Institute: ATIC
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ATIC in cancer cell metabolism1. Duval N, Luhrs K, Wilkinson TG, 2nd, Baresova V, Skopova V, et al. (2013) Genetic and metabolomic analysis of AdeD and AdeI mutants of de novo purine biosynthesis: cellular models of de novo purine biosynthesis deficiency disorders. Mol Genet Metab 108: 178-189. doi: 10.1016/j.ymgme.2013.01.002. pmid: 4296673. go to article

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Phenotypic Information for ATIC(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ATIC
Familial Cancer Database: ATIC
* 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 601731; gene.
608688; phenotype.
Orphanet 250977; AICA-ribosiduria.
DiseaseKEGG Disease: ATIC
MedGen: ATIC (Human Medical Genetics with Condition)
ClinVar: ATIC
PhenotypeMGI: ATIC (International Mouse Phenotyping Consortium)
PhenomicDB: ATIC

Mutations for ATIC
* 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
ovaryATICchr2216187830216187850ABCA12chr2215916028215916048
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 ATIC related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB224490ATIC12862216176804216182957NAB12855372191518452191523904
BC007306SNUPN14731497157591863275918656ATIC148933972216176838216214479
BU675973ATIC181182216214387216214487ATIC1132362216214262216214385
BE144253EFNB2268413107163028107163086ATIC785762216212908216213407

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 # sample2         1      
GAIN (# sample)1         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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=4)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr2:216189997-216189997p.K108K1
chr2:216190751-216190751p.R141*1
chr2:216198130-216198130p.D291V1
chr2:216200820-216200820p.K357K1
chr2:216203553-216203553p.L384F1
chr2:216214270-216214270p.A557A1
chr2:216177279-216177279p.A26A1
chr2:216177302-216177302p.S34F1

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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=12

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 22  2 1  523  510 14
# mutation31 13  2 1  523  511 13
nonsynonymous SNV11 9  2    412  47 8
synonymous SNV2  4    1  111  14 5
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
chr2:216203555p.L384L6
chr2:216203554p.L384P5
chr2:216203539p.R379Q3
chr2:216191614p.V201I3
chr2:216211546p.A462V2
chr2:216177302p.V18M1
chr2:216200802p.V153V1
chr2:216190051p.E348K1
chr2:216211586p.P516S1
chr2:216197147p.S34P1

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 ATIC 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 ATIC

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

AAMP,ATIC,C2orf47,COQ5,DNPEP,METTL21A,EEF2KMT,
FARSB,GMPPA,GRPEL1,MRPL44,NDUFA10,NDUFB3,NIF3L1,
ORMDL2,PSMD14,PSMD1,RPE,SMARCAL1,SUMO1,XRCC5
ATIC,MISP,DBNDD1,ETNK2,FAM83A,GSS,HSPE1,
MIPEP,MRPL13,PDCL3,PDF,PRR15L,SLC50A1,SEPHS2,
SNRPD3,STARD10,NELFCD,TRUB2,TSPAN1,TSTA3,TTC39A

ATIC,BCS1L,CIAO1,CPSF3,HSPD1,METTL5,MFF,
NIFK,MRPL30,MTIF2,NOL10,NOP58,OLA1,PNPT1,
SLC5A6,SMYD5,SSB,WDR12,WDR75,XRCC5,ZC3H15
ATAD2,ATIC,BUB1B,DTL,E2F1,EXOSC10,LMNB1,
MCM2,MCM4,MCM7,MTHFD1,NAT10,NCAPD3,NUP155,
PAICS,PRPF19,RRM1,SCFD2,SSRP1,TRAP1,WDHD1
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 ATIC
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P31939; -.
ChemistryChEMBL CHEMBL2518; -.
Organism-specific databasesPharmGKB PA25094; -.
Organism-specific databasesCTD 471; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB001165-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; nutraceuticalTetrahydrofolic acid
DB006425-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; investigationalPemetrexed
DB017005-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseexperimentalAicar
DB019725-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseexperimentalGuanosine-5'-Monophosphate
DB023095-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseexperimental5--Monophosphate-9-Beta-D-Ribofuranosyl Xanthine
DB034425-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseexperimental2-[5-Hydroxy-3-Methyl-1-(2-Methyl-4-Sulfo-Phenyl)-1h-Pyrazol-4-Ylazo]-4-Sulfo-Benzoic Acid
DB040575-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseexperimentalBeta-Dadf, Msa, Multisubstrate Adduct Inhibitor
DB001455-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; nutraceuticalGlycine
DB001305-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; nutraceutical; investigationalL-Glutamine
DB001585-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; nutraceuticalFolic Acid
DB005635-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapprovedMethotrexate
DB007955-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapprovedSulfasalazine
DB006405-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseapproved; investigationalAdenosine


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Cross referenced IDs for ATIC
* 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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