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 ALDH1A1

Basic gene info.	Gene symbol	ALDH1A1
	Gene name	aldehyde dehydrogenase 1 family, member A1
	Synonyms	ALDC\|ALDH-E1\|ALDH1\|ALDH11\|HEL-9\|HEL-S-53e\|HEL12\|PUMB1\|RALDH1
	Cytomap	UCSC genome browser: 9q21.13
	Genomic location	chr9 :75515577-75568233
	Type of gene	protein-coding
	RefGenes	NM_000689.4,
	Ensembl id	ENSG00000165092
	Description	ALDH class 1ALHDIIRALDH 1acetaldehyde dehydrogenase 1aldehyde dehydrogenase 1, solublealdehyde dehydrogenase, liver cytosolicepididymis luminal protein 12epididymis luminal protein 9epididymis secretory sperm binding protein Li 53eretinal dehydro
	Modification date	20141222
dbXrefs	MIM : 100640
	HGNC : HGNC
	Ensembl : ENSG00000165092
	HPRD : 00001
	Vega : OTTHUMG00000020019
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALDH1A1
	BioGPS: 216
	Gene Expression Atlas: ENSG00000165092
	The Human Protein Atlas: ENSG00000165092
Pathway	NCI Pathway Interaction Database: ALDH1A1
	KEGG: ALDH1A1
	REACTOME: ALDH1A1
	ConsensusPathDB
	Pathway Commons: ALDH1A1
Metabolism	MetaCyc: ALDH1A1
	HUMANCyc: ALDH1A1
Regulation	Ensembl's Regulation: ENSG00000165092
	miRBase: chr9 :75,515,577-75,568,233
	TargetScan: NM_000689
	cisRED: ENSG00000165092
Context	iHOP: ALDH1A1
	cancer metabolism search in PubMed: ALDH1A1
	UCL Cancer Institute: ALDH1A1
Assigned class in ccmGDB	C

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Phenotypic Information for ALDH1A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ALDH1A1
	Familial Cancer Database: ALDH1A1

* 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_RETINOL_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ALDH1A1
	MedGen: ALDH1A1 (Human Medical Genetics with Condition)
	ClinVar: ALDH1A1
Phenotype	MGI: ALDH1A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALDH1A1

Mutations for ALDH1A1

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ALDH1A1 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
DA668305	HSPA8	2	89	11	122930043	122930129	ALDH1A1	90	558	9	75531952	75542085
BF436998	ALDH1A1	35	274	9	75515618	75515857	EPB41L4A	273	330	5	111754705	111754762
AI493829	ALDH1A1	1	21	9	75652605	75652625	ELL	8	477	19	18555203	18555674
AA515000	ALDH1A1	8	87	9	75515725	75515804	ALDH1A1	81	217	9	75515589	75515725
BQ317586	ALDH1A1	23	244	9	75540456	75543894	ALDH1A1	238	333	9	75545800	75545895
BU674486	ALDH1A1	19	132	9	75515585	75515698	ALDH1A1	122	538	9	75515748	75516164
DA896624	ALDH1A1	1	475	9	75531935	75567934	ALDH1A1	469	540	9	75540406	75540477
BU685483	ALDH1A1	18	129	9	75515587	75515698	ALDH1A1	119	577	9	75515706	75516164

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

There's no copy number variation information in COSMIC data for this gene.

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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=44)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr9:75539039-75539039	p.P215S	3
chr9:75545879-75545879	p.P76P	2
chr9:75520915-75520915	p.C464C	2
chr9:75520934-75520934	p.G458D	2
chr9:75567907-75567907	p.S4A	1
chr9:75526891-75526891	p.R395C	1
chr9:75540481-75540481	p.L184L	1
chr9:75543930-75543930	p.E107G	1
chr9:75527039-75527039	p.?	1
chr9:75524517-75524517	p.?	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	4	6		10	1		1		3			5	1	3			3	6		9
# mutation	4	6		10	1		1		3			5	1	3			3	6		10
nonsynonymous SNV	2	2		9	1				1			4					3	2		8
synonymous SNV	2	4		1			1		2			1	1	3				4		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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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
chr9:75531989	p.S4A	1
chr9:75520915	p.G473A	1
chr9:75540496	p.P344S	1
chr9:75526976	p.P182P	1
chr9:75555069	p.S3S	1
chr9:75533640	p.C464C	1
chr9:75520934	p.G333E	1
chr9:75542069	p.K179K	1
chr9:75526981	p.G458D	1
chr9:75555088	p.A306T	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 ALDH1A1 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 ALDH1A1

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


ABCA6,ABCA9,ALDH1A1,C10orf128,CCDC80,CHRDL1,CLEC1A, DOCK11,FLI1,FREM1,GIMAP6,GIMAP8,HTR2B,IGF1, KCNS2,KCTD12,LHFP,MFAP4,PDE1A,SLC9A9,ZEB2	ALDH1A1,CHRDL1,CREBL2,DIRC3,ECM2,GTDC1,HNMT, ITGB1,MAN1A1,NEK7,OSTM1,PALM2-AKAP2,PGRMC2,PTPRQ, RGS22,SEPT11,SERINC1,SH3D19,TIMP3,VAMP3,VGLL3

ABCB6,ALDH1A1,COLCA1,FAM222A,LINC00261,CA8,CACNA1B, CALML6,CDK6,HPCAL1,HPN,HS3ST5,IGF2-AS,IFNL2, INS,JPH1,KIAA1324,LIN7A,LOC100128675,SOX2,TRIM71	ALDH1A1,ANO6,AQP1,C4orf3,CYP2U1,FAM172A,GRIK2, IMMP2L,ISCU,KCTD3,LMO4,PFN2,CPQ,PLA2G4C, SEC22C,STK33,TMEM64,VKORC1,WRB,ZNF16,ZNF639

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 ALDH1A1

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
DB00157	aldehyde dehydrogenase 1 family, member A1	approved; nutraceutical	NADH
DB00162	aldehyde dehydrogenase 1 family, member A1	approved; nutraceutical	Vitamin A
DB00755	aldehyde dehydrogenase 1 family, member A1	approved; nutraceutical; investigational	Tretinoin
DB01907	aldehyde dehydrogenase 1 family, member A1	experimental	Nicotinamide-Adenine-Dinucleotide
DB04447	aldehyde dehydrogenase 1 family, member A1	experimental	1,4-Dithiothreitol
DB00958	aldehyde dehydrogenase 1 family, member A1	approved	Carboplatin
DB04572	aldehyde dehydrogenase 1 family, member A1	approved	Thiotepa
DB00531	aldehyde dehydrogenase 1 family, member A1	approved; investigational	Cyclophosphamide

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Cross referenced IDs for ALDH1A1

* 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