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 symbolALDH1A1
Gene namealdehyde dehydrogenase 1 family, member A1
SynonymsALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1
CytomapUCSC genome browser: 9q21.13
Genomic locationchr9 :75515577-75568233
Type of geneprotein-coding
RefGenesNM_000689.4,
Ensembl idENSG00000165092
DescriptionALDH 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 date20141222
dbXrefs MIM : 100640
HGNC : HGNC
Ensembl : ENSG00000165092
HPRD : 00001
Vega : OTTHUMG00000020019
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH1A1
BioGPS: 216
Gene Expression Atlas: ENSG00000165092
The Human Protein Atlas: ENSG00000165092
PathwayNCI Pathway Interaction Database: ALDH1A1
KEGG: ALDH1A1
REACTOME: ALDH1A1
ConsensusPathDB
Pathway Commons: ALDH1A1
MetabolismMetaCyc: ALDH1A1
HUMANCyc: ALDH1A1
RegulationEnsembl's Regulation: ENSG00000165092
miRBase: chr9 :75,515,577-75,568,233
TargetScan: NM_000689
cisRED: ENSG00000165092
ContextiHOP: ALDH1A1
cancer metabolism search in PubMed: ALDH1A1
UCL Cancer Institute: ALDH1A1
Assigned class in ccmGDBC

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Phenotypic Information for ALDH1A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_RETINOL_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALDH1A1
MedGen: ALDH1A1 (Human Medical Genetics with Condition)
ClinVar: ALDH1A1
PhenotypeMGI: ALDH1A1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ALDH1A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA668305HSPA828911122930043122930129ALDH1A19055897553195275542085
BF436998ALDH1A13527497551561875515857EPB41L4A2733305111754705111754762
AI493829ALDH1A112197565260575652625ELL8477191855520318555674
AA515000ALDH1A188797551572575515804ALDH1A18121797551558975515725
BQ317586ALDH1A12324497554045675543894ALDH1A123833397554580075545895
BU674486ALDH1A11913297551558575515698ALDH1A112253897551574875516164
DA896624ALDH1A1147597553193575567934ALDH1A146954097554040675540477
BU685483ALDH1A11812997551558775515698ALDH1A111957797551570675516164

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

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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=3

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check002.gifSomatic 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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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
chr9:75539039-75539039p.P215S3
chr9:75520915-75520915p.C464C2
chr9:75520934-75520934p.G458D2
chr9:75545879-75545879p.P76P2
chr9:75543859-75543859p.R131C1
chr9:75526981-75526981p.G365R1
chr9:75545838-75545838p.Y90C1
chr9:75516194-75516194p.G479V1
chr9:75531990-75531990p.G294V1
chr9:75540461-75540461p.V191A1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample46 101 1 3  513  36 9
# mutation46 101 1 3  513  36 10
nonsynonymous SNV22 91   1  4    32 8
synonymous SNV24 1  1 2  113   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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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
chr9:75545819p.T6M1
chr9:75526929p.G479V1
chr9:75531961p.L357L1
chr9:75516186p.L184L1
chr9:75540464p.S4A1
chr9:75545838p.G473A1
chr9:75526946p.P344S1
chr9:75531968p.P182P1
chr9:75516194p.S3S1
chr9:75540481p.C464C1

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 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

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

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
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 ALDH1A1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157aldehyde dehydrogenase 1 family, member A1approved; nutraceuticalNADH
DB00162aldehyde dehydrogenase 1 family, member A1approved; nutraceuticalVitamin A
DB00755aldehyde dehydrogenase 1 family, member A1approved; nutraceutical; investigationalTretinoin
DB01907aldehyde dehydrogenase 1 family, member A1experimentalNicotinamide-Adenine-Dinucleotide
DB04447aldehyde dehydrogenase 1 family, member A1experimental1,4-Dithiothreitol
DB00958aldehyde dehydrogenase 1 family, member A1approvedCarboplatin
DB04572aldehyde dehydrogenase 1 family, member A1approvedThiotepa
DB00531aldehyde dehydrogenase 1 family, member A1approved; investigationalCyclophosphamide


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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



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