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 ADI1

Basic gene info.	Gene symbol	ADI1
	Gene name	acireductone dioxygenase 1
	Synonyms	APL1\|ARD\|Fe-ARD\|MTCBP1\|Ni-ARD\|SIPL\|mtnD
	Cytomap	UCSC genome browser: 2p25.3
	Genomic location	chr2 :3501689-3523350
	Type of gene	protein-coding
	RefGenes	NM_018269.3,
	Ensembl id	ENSG00000182551
	Description	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenaseARDMT1-MMP cytoplasmic tail-binding protein-1MTCBP-1acireductone dioxygenase (Fe(2+)-requiring)acireductone dioxygenase (Ni(2+)-requiring)fe-ARDmembrane-type 1 matrix metalloproteinase cytoplasmic
	Modification date	20141207
dbXrefs	MIM : 613400
	HGNC : HGNC
	Ensembl : ENSG00000182551
	HPRD : 17607
	Vega : OTTHUMG00000112441
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADI1
	BioGPS: 55256
	Gene Expression Atlas: ENSG00000182551
	The Human Protein Atlas: ENSG00000182551
Pathway	NCI Pathway Interaction Database: ADI1
	KEGG: ADI1
	REACTOME: ADI1
	ConsensusPathDB
	Pathway Commons: ADI1
Metabolism	MetaCyc: ADI1
	HUMANCyc: ADI1
Regulation	Ensembl's Regulation: ENSG00000182551
	miRBase: chr2 :3,501,689-3,523,350
	TargetScan: NM_018269
	cisRED: ENSG00000182551
Context	iHOP: ADI1
	cancer metabolism search in PubMed: ADI1
	UCL Cancer Institute: ADI1
Assigned class in ccmGDB	C

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Phenotypic Information for ADI1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ADI1
	Familial Cancer Database: ADI1

* 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_CYSTEINE_AND_METHIONINE_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES

Others
OMIM
Orphanet
Disease	KEGG Disease: ADI1
	MedGen: ADI1 (Human Medical Genetics with Condition)
	ClinVar: ADI1
Phenotype	MGI: ADI1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ADI1

Mutations for ADI1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ADI1	chr2	3521582	3521602		chr8	128759951	128759971

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 ADI1 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
BM353985	ADI1	12	72	2	3502395	3502455	ADI1	70	181	2	3502303	3502414
AA351447	ZNF626	1	90	19	20844250	20844339	ADI1	90	406	2	3504625	3518634
BF095880	ADI1	1	432	2	3502501	3504659	TUBB6	429	487	18	12326076	12326134
CK904967	ADI1	1	189	2	3502226	3502414	ADI1	187	247	2	3502395	3502455
CV569358	ADI1	44	478	2	3502350	3502784	ADI1	472	588	2	3502224	3502339
BM456873	ADI1	2	77	2	3523204	3523279	TRIM14	70	877	9	100848713	100849516

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=6)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr2:3504687-3504687	p.D106D	3
chr2:3502845-3502845	p.T143T	3
chr2:3502844-3502844	p.K144E	2
chr2:3517712-3517712	p.L52L	2
chr2:3504627-3504627	p.T126T	1
chr2:3504654-3504654	p.I117I	1
chr2:3504658-3504658	p.R116Q	1
chr2:3502771-3502771	p.R168H	1
chr2:3504690-3504690	p.F105F	1
chr2:3517692-3517692	p.R59K	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=2

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		1			3		1			3	1		1
# mutation				3			1		1			3		1			3	1		1
nonsynonymous SNV				2					1			1		1			2	1
synonymous SNV				1			1					2					1			1

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
chr2:3504690	p.K144E	2
chr2:3502844	p.F105F	2
chr2:3504658	p.R96S	1
chr2:3504681	p.E47E	1
chr2:3502771	p.R168L	1
chr2:3504719	p.T143T	1
chr2:3517727	p.Y142C	1
chr2:3502845	p.T136M	1
chr2:3502849	p.R134C	1
chr2:3504598	p.P128P	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 ADI1 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 ADI1

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


ACP1,ADI1,C12orf45,PTRHD1,COMMD1,COX4I1,CPSF3, DGUOK,DTNB,FAM58A,MFSD2B,NOL10,PDIA6,RNASEH1, RPS7,SF3B14,SNRPG,TSSC1,TRAPPC12,UQCRH,UQCRHL	ACOT13,ACTR1A,ADI1,ATP5G3,ATP5H,ATP5J,ATP6V1E1, C22orf39,PRADC1,CYSTM1,CHCHD4,EIF2B3,GTF3A,LDHA, MGST3,MSRB2,NDUFA6,PSMC1,RILP,SLC25A20,SNAPIN

ACP1,ADI1,COX14,PTRHD1,CISD2,CNIH1,COMMD1, COX6A1,COX7A2L,DUSP11,MDH1,MRPL44,MRPL54,MYEOV2, NDUFS3,NOP10,ORC4,OST4,POLE4,PPA2,SUCLG1	ADI1,BDH2,LINC00324,TMEM256,SMIM20,CCNG1,CENPV, CRADD,DERA,DGCR6,ETV2,GLOD4,HACL1,HOXB7, IGBP1,LOC201651,NDFIP1,PIGH,RARS2,RNF141,TMEM219

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 ADI1

There's no related Drug.

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Cross referenced IDs for ADI1

* 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