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 ALDH1A3
Basic gene info.Gene symbolALDH1A3
Gene namealdehyde dehydrogenase 1 family, member A3
SynonymsALDH1A6|ALDH6|MCOP8|RALDH3
CytomapUCSC genome browser: 15q26.3
Genomic locationchr15 :101420008-101456830
Type of geneprotein-coding
RefGenesNM_000693.3,
NM_001293815.1,NM_001037224.1,
Ensembl idENSG00000184254
Descriptionacetaldehyde dehydrogenase 6aldehyde dehydrogenase 6aldehyde dehydrogenase family 1 member A3retinaldehyde dehydrogenase 3
Modification date20141207
dbXrefs MIM : 600463
HGNC : HGNC
Ensembl : ENSG00000184254
HPRD : 02713
Vega : OTTHUMG00000186439
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH1A3
BioGPS: 220
Gene Expression Atlas: ENSG00000184254
The Human Protein Atlas: ENSG00000184254
PathwayNCI Pathway Interaction Database: ALDH1A3
KEGG: ALDH1A3
REACTOME: ALDH1A3
ConsensusPathDB
Pathway Commons: ALDH1A3
MetabolismMetaCyc: ALDH1A3
HUMANCyc: ALDH1A3
RegulationEnsembl's Regulation: ENSG00000184254
miRBase: chr15 :101,420,008-101,456,830
TargetScan: NM_000693
cisRED: ENSG00000184254
ContextiHOP: ALDH1A3
cancer metabolism search in PubMed: ALDH1A3
UCL Cancer Institute: ALDH1A3
Assigned class in ccmGDBC

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Phenotypic Information for ALDH1A3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH1A3
Familial Cancer Database: ALDH1A3
* 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_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_HISTIDINE_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_PHENYLALANINE_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALDH1A3
MedGen: ALDH1A3 (Human Medical Genetics with Condition)
ClinVar: ALDH1A3
PhenotypeMGI: ALDH1A3 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH1A3

Mutations for ALDH1A3
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasALDH1A3chr15101435513101435533ALDH1A3chr15101448265101448285
pancreasALDH1A3chr15101444218101444238ALDH1A3chr15101444893101444913
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ALDH1A3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU675142ALDH1A31832615101456519101456827ALDH1A332148515101456364101456528
BU608092ALDH1A31711215101452037101452132ALDH1A310918015101451947101452018

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        2        
GAIN (# sample)        2        
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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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=47)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=1)

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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
chr15:101438350-101438350p.K284fs*834
chr15:101427793-101427793p.A74V3
chr15:101427829-101427829p.S86L3
chr15:101433160-101433160p.V162V2
chr15:101433167-101433167p.F165I2
chr15:101432712-101432712p.?2
chr15:101447368-101447368p.E426K2
chr15:101454947-101454947p.V503A2
chr15:101427864-101427864p.R98W2
chr15:101448629-101448629p.A470T2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 133 211 1511 225 10
# mutation13 123 311 1711 236 11
nonsynonymous SNV 3 103     13 1 125 8
synonymous SNV1  2  311  41  111 3
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
chr15:101454947p.V396A,ALDH1A33
chr15:101427779p.P69P,ALDH1A32
chr15:101427864p.R98W,ALDH1A32
chr15:101432746p.K47E,ALDH1A31
chr15:101445832p.F182V1
chr15:101434200p.A191S,ALDH1A31
chr15:101454917p.D329N,ALDH1A31
chr15:101425511p.T51I,ALDH1A31
chr15:101440788p.F182F1
chr15:101432769p.A195A,ALDH1A31

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 ALDH1A3 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 ALDH1A3

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

ALDH1A3,NCMAP,CD14,CD180,DMBT1,DOK5,DPP4,
GPRC5B,IGFL4,LIPG,MPZL2,MRGPRX3,NOS1,PAK3,
PDE11A,PGA5,PTN,TGFBR2,TMEM233,VNN1,XDH
ALDH1A3,AMD1,ARF6,ARFGAP3,BBOX1,PLEKHS1,SPTSSA,
EVA1C,CCDC6,CLDN1,CRY1,CTSV,GCNT1,KCNK2,
KRT80,MAPK1IP1L,MPZL2,SOCS5,TES,TMEM27,WEE1

ALDH1A3,BHMT2,CDO1,EFEMP1,FBLN5,GPR133,INMT,
ITIH5,LHFP,LTBP2,MAN1C1,MGP,PDE1A,PODN,
PRICKLE1,PTGER3,PTGIS,RBMS3,RNF180,RUNX1T1,SLIT3
ALDH1A3,C7,CDH19,CDO1,ELOVL2,EYA4,FAM126A,
FGF1,GPM6B,LHFP,RANBP3L,SEC22C,SLC35F1,SNCA,
SNCG,RNF217-AS1,SYDE2,SLC35G2,TMEM88,TMOD2,ZNF483
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 ALDH1A3
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 A3approved; nutraceuticalNADH
DB00162aldehyde dehydrogenase 1 family, member A3approved; nutraceuticalVitamin A


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Cross referenced IDs for ALDH1A3
* 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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