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 ALDH3A2
Basic gene info.Gene symbolALDH3A2
Gene namealdehyde dehydrogenase 3 family, member A2
SynonymsALDH10|FALDH|SLS
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :19552063-19580904
Type of geneprotein-coding
RefGenesNM_000382.2,
NM_001031806.1,
Ensembl idENSG00000072210
Descriptionaldehyde dehydrogenase 10aldehyde dehydrogenase family 3 member A2fatty aldehyde dehydrogenasemicrosomal aldehyde dehydrogenase
Modification date20141207
dbXrefs MIM : 609523
HGNC : HGNC
Ensembl : ENSG00000072210
HPRD : 07188
Vega : OTTHUMG00000059471
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH3A2
BioGPS: 224
Gene Expression Atlas: ENSG00000072210
The Human Protein Atlas: ENSG00000072210
PathwayNCI Pathway Interaction Database: ALDH3A2
KEGG: ALDH3A2
REACTOME: ALDH3A2
ConsensusPathDB
Pathway Commons: ALDH3A2
MetabolismMetaCyc: ALDH3A2
HUMANCyc: ALDH3A2
RegulationEnsembl's Regulation: ENSG00000072210
miRBase: chr17 :19,552,063-19,580,904
TargetScan: NM_000382
cisRED: ENSG00000072210
ContextiHOP: ALDH3A2
cancer metabolism search in PubMed: ALDH3A2
UCL Cancer Institute: ALDH3A2
Assigned class in ccmGDBC

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Phenotypic Information for ALDH3A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH3A2
Familial Cancer Database: ALDH3A2
* 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_ASCORBATE_AND_ALDARATE_METABOLISM
KEGG_FATTY_ACID_METABOLISM
KEGG_ARGININE_AND_PROLINE_METABOLISM
KEGG_HISTIDINE_METABOLISM
KEGG_TRYPTOPHAN_METABOLISM
KEGG_BETA_ALANINE_METABOLISM
KEGG_GLYCEROLIPID_METABOLISM
KEGG_PYRUVATE_METABOLISM
KEGG_PROPANOATE_METABOLISM
KEGG_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALDH3A2
MedGen: ALDH3A2 (Human Medical Genetics with Condition)
ClinVar: ALDH3A2
PhenotypeMGI: ALDH3A2 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH3A2

Mutations for ALDH3A2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
haematopoietic_and_lymphoid_tissueALDH3A2chr171956250319562503ALDH3A2chr171956250319562503
pancreasALDH3A2chr171957446019574480MYO1Dchr173084901030849030
pancreasALDH3A2chr171957723719577257B9D1chr171927149719271517
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 ALDH3A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF854270NEAT18253116519443965194684ALDH3A2245444171956698919567188
BF845221ALDH3A214299171955874119559029SMC1A296578X5343873953439114
AV652827ALDH3A21534171956930719569840LOC646214530727152193356321933818
AI769187ATP1B211121775602937560404ALDH3A2108276171955213519552303

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 # sample1  1    1        
GAIN (# sample)1  1    1        
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=4

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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=12)
Stat. for Deletions
(# total SNVs=1)
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
chr17:19575149-19575149p.P441P3
chr17:19568332-19568332p.T393T3
chr17:19559759-19559759p.T184T2
chr17:19559761-19559761p.G185V2
chr17:19555901-19555901p.T143fs*132
chr17:19568264-19568264p.I371V2
chr17:19575075-19575075p.D417H2
chr17:19568265-19568265p.I371T2
chr17:19564539-19564539p.I300L2
chr17:19564573-19564573p.R311H2

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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
# sample   13  1 22 4 3 125 4
# mutation   11  1 22 4 3 125 5
nonsynonymous SNV   9    22 3 2  25 3
synonymous SNV   2  1    1 1 1   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
chr17:19575149p.P441P,ALDH3A23
chr17:19568264p.I371V,ALDH3A22
chr17:19568265p.I371T,ALDH3A22
chr17:19555892p.L159I,ALDH3A21
chr17:19566754p.P398T,ALDH3A21
chr17:19575085p.S404F,ALDH3A21
chr17:19555900p.E168K,ALDH3A21
chr17:19566800p.T418I,ALDH3A21
chr17:19575092p.Q176R,ALDH3A21
chr17:19555901p.S420Y,ALDH3A21

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 ALDH3A2 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 ALDH3A2

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

ACADSB,AKAP10,ALDH3A2,ZFAND4,ANXA9,AP1AR,B9D1,
COQ7,EPN2,FLNB,GIN1,KRT37,PEX12,SFXN2,
SGK3,SIAH2,SLC27A2,SNX24,STC2,SYBU,ULK2
ALDH3A2,CLMP,ASPH,ATP9A,BHMT2,BTD,MTURN,
CCDC69,DHDDS,DMGDH,FOXN3,MRAS,PLXNA4,PYGL,
SNN,SORBS1,TK2,TLN2,TNS1,TTC7B,VKORC1L1

AKAP10,ALDH3A1,ALDH3A2,B9D1,CYSTM1,CLDN7,SPECC1,
DHRS7B,EPN2,GCGR,MAPK7,MED11,MPDU1,PLIN5,
SNORA11E,TMEM102,TMEM11,TNK1,TRIM16,ULK2,USP22
ABHD5,ACOT4,ADH1C,AGMAT,ALDH3A2,APMAP,C2orf47,
DNAJC25,ETFA,FAM45A,FDX1,GCLM,KCNV1,ME2,
MTCH2,PEX11A,PHYH,PITX2,RPP25,SLC27A2,TMEM139
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 ALDH3A2
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 A2approved; nutraceuticalNADH


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Cross referenced IDs for ALDH3A2
* 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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