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 ALDH3A1
Basic gene info.Gene symbolALDH3A1
Gene namealdehyde dehydrogenase 3 family, member A1
SynonymsALDH3|ALDHIII
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :19641297-19648925
Type of geneprotein-coding
RefGenesNM_000691.4,
NM_001135167.1,NM_001135168.1,
Ensembl idENSG00000108602
Descriptionaldehyde dehydrogenase isozyme 3aldehyde dehydrogenase type IIIaldehyde dehydrogenase, dimeric NADP-preferringstomach aldehyde dehydrogenase
Modification date20141207
dbXrefs MIM : 100660
HGNC : HGNC
Ensembl : ENSG00000108602
HPRD : 00004
Vega : OTTHUMG00000059469
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH3A1
BioGPS: 218
Gene Expression Atlas: ENSG00000108602
The Human Protein Atlas: ENSG00000108602
PathwayNCI Pathway Interaction Database: ALDH3A1
KEGG: ALDH3A1
REACTOME: ALDH3A1
ConsensusPathDB
Pathway Commons: ALDH3A1
MetabolismMetaCyc: ALDH3A1
HUMANCyc: ALDH3A1
RegulationEnsembl's Regulation: ENSG00000108602
miRBase: chr17 :19,641,297-19,648,925
TargetScan: NM_000691
cisRED: ENSG00000108602
ContextiHOP: ALDH3A1
cancer metabolism search in PubMed: ALDH3A1
UCL Cancer Institute: ALDH3A1
Assigned class in ccmGDBC

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Phenotypic Information for ALDH3A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH3A1
Familial Cancer Database: ALDH3A1
* 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: ALDH3A1
MedGen: ALDH3A1 (Human Medical Genetics with Condition)
ClinVar: ALDH3A1
PhenotypeMGI: ALDH3A1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH3A1

Mutations for ALDH3A1
* 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 ALDH3A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV572132MSI21261175533438555335694ALDH3A1253378171964130319641428
BQ331769DDX55116312124099741124101096ALDH3A1156289171964364919643782
BU679486ALDH3A11883171964130219641367ASPH7345886257429862596725
BU685263ALDH3A11883171964130219641367ASPH7351386257424362596725

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=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
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
chr17:19646651-19646651p.D96D2
chr17:19648427-19648427p.E6K2
chr17:19643782-19643782p.Y272Y2
chr17:19641725-19641725p.E420K2
chr17:19642335-19642335p.L397S2
chr17:19643676-19643676p.T308P2
chr17:19644516-19644516p.A233T2
chr17:19642827-19642827p.N370N2
chr17:19643762-19643762p.S279F1
chr17:19641649-19641649p.P445fs*61

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  53   1  412  95 8
# mutation1  53   1  412  96 8
nonsynonymous SNV1  52      312  56 4
synonymous SNV    1   1  1    4  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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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
chr17:19645413p.L439L,ALDH3A11
chr17:19641670p.N239I,ALDH3A11
chr17:19646621p.V110V,ALDH3A11
chr17:19643674p.G438D,ALDH3A11
chr17:19645423p.F237L,ALDH3A11
chr17:19641686p.G106G,ALDH3A11
chr17:19646675p.L433V,ALDH3A11
chr17:19643780p.A233T,ALDH3A11
chr17:19645437p.E88D,ALDH3A11
chr17:19641725p.E420K,ALDH3A11

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 ALDH3A1 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 ALDH3A1

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

AKR1B10,ALDH3A1,BCL2L10,GAGE12J,GAGE13,GAGE2B,GAGE8,
GPX2,HOXD11,IQCF2,KRT13,LOC285629,NKX2-4,OPALIN,
RBMXL2,SLC47A2,UGT1A5,VCX,VCX3A,VCX3B,VCY
ADH7,AKR1B10,ALDH3A1,CAPNS2,CYP4F3,GJB6,KRT13,
KRT4,KRT6A,KRT78,KRTDAP,SERPINB3,SOX2,SPRR1A,
SPRR2A,SPRR2D,SPRR3,TMPRSS4,UGT1A6,UGT1A7,UPK1B

GGACT,ALDH3A1,ALDH3A2,ART1,ADTRP,CCDC154,DHRS7B,
FGFBP1,GCGR,HOXA2,MAPK7,NXNL2,PLIN5,SLC47A2,
SNORA11E,TMEM11,UGT1A10,UGT1A6,UGT1A7,UGT1A9,USP22
ADH1C,ALDH3A1,BDH1,APMAP,C21orf33,CA2,CLYBL,
DTWD2,GSS,LOC100134229,ME3,NDUFA10,NDUFV1,PCCA,
PEX11A,RPL10L,RPP25,STARD7,TBRG4,TCEA3,WARS2
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 ALDH3A1
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 3 family, member A1approved; nutraceuticalNADH
DB01907aldehyde dehydrogenase 3 family, member A1experimentalNicotinamide-Adenine-Dinucleotide
DB00958aldehyde dehydrogenase 3 family, member A1approvedCarboplatin
DB04572aldehyde dehydrogenase 3 family, member A1approvedThiotepa
DB00531aldehyde dehydrogenase 3 family, member A1approved; investigationalCyclophosphamide


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Cross referenced IDs for ALDH3A1
* 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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