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 AKR1A1

Basic gene info.	Gene symbol	AKR1A1
	Gene name	aldo-keto reductase family 1, member A1 (aldehyde reductase)
	Synonyms	ALDR1\|ALR\|ARM\|DD3\|HEL-S-6
	Cytomap	UCSC genome browser: 1p33-p32
	Genomic location	chr1 :46016454-46035723
	Type of gene	protein-coding
	RefGenes	NM_001202414.1, NM_006066.3,NM_153326.2,NM_001202413.1,
	Ensembl id	ENSG00000117448
	Description	HEL-S-165mPalcohol dehydrogenasealcohol dehydrogenase [NADP(+)]aldehyde reductasealdo-keto reductase family 1 member A1dihydrodiol dehydrogenase 3epididymis secretory protein Li 6epididymis secretory sperm binding protein Li 165mP
	Modification date	20141207
dbXrefs	MIM : 103830
	HGNC : HGNC
	Ensembl : ENSG00000117448
	HPRD : 00069
	Vega : OTTHUMG00000007740
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AKR1A1
	BioGPS: 10327
	Gene Expression Atlas: ENSG00000117448
	The Human Protein Atlas: ENSG00000117448
Pathway	NCI Pathway Interaction Database: AKR1A1
	KEGG: AKR1A1
	REACTOME: AKR1A1
	ConsensusPathDB
	Pathway Commons: AKR1A1
Metabolism	MetaCyc: AKR1A1
	HUMANCyc: AKR1A1
Regulation	Ensembl's Regulation: ENSG00000117448
	miRBase: chr1 :46,016,454-46,035,723
	TargetScan: NM_001202414
	cisRED: ENSG00000117448
Context	iHOP: AKR1A1
	cancer metabolism search in PubMed: AKR1A1
	UCL Cancer Institute: AKR1A1
Assigned class in ccmGDB	C

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Phenotypic Information for AKR1A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AKR1A1
	Familial Cancer Database: AKR1A1

* 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_GLYCOLYSIS_GLUCONEOGENESIS KEGG_GLYCEROLIPID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: AKR1A1
	MedGen: AKR1A1 (Human Medical Genetics with Condition)
	ClinVar: AKR1A1
Phenotype	MGI: AKR1A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AKR1A1

Mutations for AKR1A1

* 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
ovary	AKR1A1	chr1	46025669	46025689	ITPK1	chr14	93425981	93426001

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 AKR1A1 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
AI110770	AKR1A1	7	518	1	46033008	46033519	MED20	517	634	6	41874553	41874670
BF876342	AKR1A1	18	273	1	46033778	46034033	AKR1A1	269	393	1	46034458	46034582
AF116602	AKR1A1	7	518	1	46033008	46033519	MED20	517	2095	6	41873092	41874670
AF074677	AKR1A1	7	518	1	46033008	46033519	MED20	517	634	6	41874553	41874670
AW613413	AKR1A1	10	231	1	46034837	46035719	CBY1	224	467	22	39067484	39067727

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=17)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr1:46027470-46027470	p.A2T	2
chr1:46034808-46034808	p.?	2
chr1:46034238-46034238	p.P212S	2
chr1:46033709-46033709	p.T138S	1
chr1:46034266-46034266	p.R221H	1
chr1:46027472-46027472	p.A2A	1
chr1:46034829-46034829	p.T280T	1
chr1:46033748-46033748	p.V151M	1
chr1:46034294-46034294	p.E230E	1
chr1:46027485-46027485	p.L7L	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	2			2	1				1			2	2	2		1	4	1	1	5
# mutation	2			2	1				1			2	2	2		1	3	1	1	5
nonsynonymous SNV					1				1					2		1	2	1		1
synonymous SNV	2			2								2	2				1		1	4

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
chr1:46034238	p.P212S,AKR1A1	2
chr1:46027470	p.A2T,AKR1A1	1
chr1:46034216	p.Y241H,AKR1A1	1
chr1:46035600	p.A2A,AKR1A1	1
chr1:46027472	p.I259I,AKR1A1	1
chr1:46035610	p.L7L,AKR1A1	1
chr1:46027485	p.I261I,AKR1A1	1
chr1:46034256	p.G11R,AKR1A1	1
chr1:46035615	p.P262P,AKR1A1	1
chr1:46027497	p.P26P,AKR1A1	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 AKR1A1 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 AKR1A1

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


AKR1A1,ATP6V0B,ATPIF1,AURKAIP1,C1orf123,PRADC1,COPE, EDF1,GALE,GMPPA,HECTD3,LSM10,LYPLA2,MRPL41, NAGK,PARK7,SEC61B,SRA1,TMEM53,UROD,ZBTB8OS	ADAM2,AFMID,AKR1A1,ALOX15B,B3GAT1,DHCR7,DHRS2, EBP,FDPS,G6PD,GGT1,GGTLC2,GUSB,HAAO, HIST1H3D,MFSD7,MVD,MVK,PNLIPRP3,SERHL2,SERHL

ADPRHL2,AKR1A1,AURKAIP1,SMIM12,C1orf50,COQ4,ECI1, DPM3,EIF3I,LAMTOR5,IFI27L1,NDUFA6,OSGEP,PEF1, PPCS,PSMD9,RER1,SCO2,TMEM125,TSPO,TXN2	ACY3,AKR1A1,FUOM,TMEM256,IDNK,CBR1,DDC, DHRS4L2,F11,RMDN3,GALK1,GCHFR,HACL1,MMEL1, MOCOS,PFKFB4,SAT2,SERPINA1,SLC37A4,TFEC,TMEM92

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 AKR1A1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB01907	aldo-keto reductase family 1, member A1 (aldehyde reductase)	experimental	Nicotinamide-Adenine-Dinucleotide
DB02383	aldo-keto reductase family 1, member A1 (aldehyde reductase)	experimental	Tolrestat
DB03461	aldo-keto reductase family 1, member A1 (aldehyde reductase)	experimental	2'-Monophosphoadenosine 5'-Diphosphoribose
DB00997	aldo-keto reductase family 1, member A1 (aldehyde reductase)	approved; investigational	Doxorubicin

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Cross referenced IDs for AKR1A1

* 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