Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	ATIC
	Gene name	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
	Synonyms	AICAR\|AICARFT\|HEL-S-70p\|IMPCHASE\|PURH
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :216176678-216214496
	Type of gene	protein-coding
	RefGenes	NM_004044.6,
	Ensembl id	ENSG00000138363
	Description	5-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 date	20141207
dbXrefs	MIM : 601731
	HGNC : HGNC
	Ensembl : ENSG00000138363
	HPRD : 03434
	Vega : OTTHUMG00000133023
Protein	UniProt: P31939 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ATIC
	BioGPS: 471
	Gene Expression Atlas: ENSG00000138363
	The Human Protein Atlas: ENSG00000138363
Pathway	NCI Pathway Interaction Database: ATIC
	KEGG: ATIC
	REACTOME: ATIC
	ConsensusPathDB
	Pathway Commons: ATIC
Metabolism	MetaCyc: ATIC
	HUMANCyc: ATIC
Regulation	Ensembl's Regulation: ENSG00000138363
	miRBase: chr2 :216,176,678-216,214,496
	TargetScan: NM_004044
	cisRED: ENSG00000138363
Context	iHOP: ATIC
	cancer metabolism search in PubMed: ATIC
	UCL Cancer Institute: ATIC
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ATIC in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM	601731; gene. 608688; phenotype.
Orphanet	250977; AICA-ribosiduria.
Disease	KEGG Disease: ATIC
	MedGen: ATIC (Human Medical Genetics with Condition)
	ClinVar: ATIC
Phenotype	MGI: ATIC (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ATIC	chr2	216187830	216187850	ABCA12	chr2	215916028	215916048

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ATIC related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
DB224490	ATIC	1	286	2	216176804	216182957	NAB1	285	537	2	191518452	191523904
BC007306	SNUPN	1473	1497	15	75918632	75918656	ATIC	1489	3397	2	216176838	216214479
BU675973	ATIC	18	118	2	216214387	216214487	ATIC	113	236	2	216214262	216214385
BE144253	EFNB2	26	84	13	107163028	107163086	ATIC	78	576	2	216212908	216213407

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr2:216189997-216189997	p.K108K	1
chr2:216190751-216190751	p.R141*	1
chr2:216198130-216198130	p.D291V	1
chr2:216200820-216200820	p.K357K	1
chr2:216203553-216203553	p.L384F	1
chr2:216214270-216214270	p.A557A	1
chr2:216177279-216177279	p.A26A	1
chr2:216177302-216177302	p.S34F	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	1		22			2		1			5	2	3			5	10		14
# mutation	3	1		13			2		1			5	2	3			5	11		13
nonsynonymous SNV	1	1		9			2					4	1	2			4	7		8
synonymous SNV	2			4					1			1	1	1			1	4		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr2:216203555	p.L384L	6
chr2:216203554	p.L384P	5
chr2:216203539	p.R379Q	3
chr2:216191614	p.V201I	3
chr2:216211546	p.A462V	2
chr2:216189966	p.S34F	1
chr2:216197139	p.T182R	1
chr2:216214333	p.L351L	1
chr2:216177302	p.A557A	1
chr2:216200802	p.S34S	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P31939; -.
Chemistry	ChEMBL	CHEMBL2518; -.
Organism-specific databases	PharmGKB	PA25094; -.
Organism-specific databases	CTD	471; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00116	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; nutraceutical	Tetrahydrofolic acid
DB00642	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; investigational	Pemetrexed
DB01700	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	experimental	Aicar
DB01972	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	experimental	Guanosine-5'-Monophosphate
DB02309	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	experimental	5--Monophosphate-9-Beta-D-Ribofuranosyl Xanthine
DB03442	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	experimental	2-[5-Hydroxy-3-Methyl-1-(2-Methyl-4-Sulfo-Phenyl)-1h-Pyrazol-4-Ylazo]-4-Sulfo-Benzoic Acid
DB04057	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	experimental	Beta-Dadf, Msa, Multisubstrate Adduct Inhibitor
DB00145	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; nutraceutical	Glycine
DB00130	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; nutraceutical; investigational	L-Glutamine
DB00158	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; nutraceutical	Folic Acid
DB00563	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved	Methotrexate
DB00795	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved	Sulfasalazine
DB00640	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	approved; investigational	Adenosine

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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