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 ALDH1A2
Basic gene info.Gene symbolALDH1A2
Gene namealdehyde dehydrogenase 1 family, member A2
SynonymsRALDH(II)|RALDH2|RALDH2-T
CytomapUCSC genome browser: 15q21.3
Genomic locationchr15 :58245621-58358121
Type of geneprotein-coding
RefGenesNM_001206897.1,
NM_003888.3,NM_170696.2,NM_170697.2,
Ensembl idENSG00000128918
DescriptionRALDH 2retinal dehydrogenase 2retinaldehyde-specific dehydrogenase type 2
Modification date20141207
dbXrefs MIM : 603687
HGNC : HGNC
Ensembl : ENSG00000128918
HPRD : 04733
Vega : OTTHUMG00000132624
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH1A2
BioGPS: 8854
Gene Expression Atlas: ENSG00000128918
The Human Protein Atlas: ENSG00000128918
PathwayNCI Pathway Interaction Database: ALDH1A2
KEGG: ALDH1A2
REACTOME: ALDH1A2
ConsensusPathDB
Pathway Commons: ALDH1A2
MetabolismMetaCyc: ALDH1A2
HUMANCyc: ALDH1A2
RegulationEnsembl's Regulation: ENSG00000128918
miRBase: chr15 :58,245,621-58,358,121
TargetScan: NM_001206897
cisRED: ENSG00000128918
ContextiHOP: ALDH1A2
cancer metabolism search in PubMed: ALDH1A2
UCL Cancer Institute: ALDH1A2
Assigned class in ccmGDBC

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Phenotypic Information for ALDH1A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH1A2
Familial Cancer Database: ALDH1A2
* 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: ALDH1A2
MedGen: ALDH1A2 (Human Medical Genetics with Condition)
ClinVar: ALDH1A2
PhenotypeMGI: ALDH1A2 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH1A2

Mutations for ALDH1A2
* 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 ALDH1A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG231914PNPO14163174602550246025651ALDH1A2161457155824580158246097
BM677567ALDH1A218204155824562758245813IGFBP51996342217541019217541455

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=57)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:58302898-58302898p.R148*3
chr15:58306099-58306099p.D107G2
chr15:58306100-58306100p.D107N2
chr15:58306465-58306465p.N44N2
chr15:58285260-58285260p.P189P2
chr15:58285144-58285144p.E228V2
chr15:58285269-58285269p.W186*2
chr15:58302913-58302913p.V143I2
chr15:58256127-58256127p.V348I2
chr15:58302914-58302914p.G142G2

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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
# sample211183 4 1  85  1159 8
# mutation211173 4 1  94  11511 12
nonsynonymous SNV111152 4 1  84  1107 9
synonymous SNV1  21      1    54 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
chr15:58247467p.H24R,ALDH1A22
chr15:58285260p.D11G,ALDH1A22
chr15:58302913p.E79K,ALDH1A22
chr15:58256130p.A18T,ALDH1A22
chr15:58357778p.V47I,ALDH1A22
chr15:58287308p.R251C,ALDH1A22
chr15:58357797p.M399I,ALDH1A22
chr15:58306099p.P93P,ALDH1A22
chr15:58357758p.P27L,ALDH1A21
chr15:58285256p.P386P,ALDH1A21

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 ALDH1A2 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 ALDH1A2

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

ALDH1A2,FAM227B,CDAN1,COPS2,CYP2C9,DTWD1,FLJ10038,
GALK2,HAUS2,HK1,LRRC57,ICE2,PIGB,BLOC1S6,
PRTG,RSL24D1,SPANXD,SPATA5L1,SUPV3L1,TCTN3,VPS26A
ALDH1A2,ANO4,BSX,CDK15,COL1A2,COL3A1,COL5A2,
COL6A6,DBX2,DCHS1,KCNA1,MAP1A,NGF,NID1,
NPC1L1,OR5M8,THBS2,TNFRSF8,TRPC5,WBSCR17,WNT2

ALDH1A2,BOLL,CHRM4,CRISP1,CYMP,EPHA8,FGF5,
HTR1B,ITLN1,KDELR3,MAGEB10,PCDHAC1,POTEC,PRSS41,
RBP3,SEPT12,SLC2A10,SPINK4,ST8SIA2,TBC1D2,ZNF488
ALDH1A2,ARMC4,CCDC144NL,CD300LG,CDH3,CHRDL2,CST11,
DOC2B,FAM169B,FAP,FCN3,MARCO,P4HA3,SBSN,
SPINK4,TIMP1,TNIP3,
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 ALDH1A2
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 A2approved; nutraceuticalNADH
DB00162aldehyde dehydrogenase 1 family, member A2approved; nutraceuticalVitamin A
DB00755aldehyde dehydrogenase 1 family, member A2approved; nutraceutical; investigationalTretinoin
DB01907aldehyde dehydrogenase 1 family, member A2experimentalNicotinamide-Adenine-Dinucleotide


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Cross referenced IDs for ALDH1A2
* 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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