Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ALDH1B1
Basic gene info.Gene symbolALDH1B1
Gene namealdehyde dehydrogenase 1 family, member B1
SynonymsALDH5|ALDHX
CytomapUCSC genome browser: 9p11.1
Genomic locationchr9 :38392660-38398662
Type of geneprotein-coding
RefGenesNM_000692.4,
Ensembl idENSG00000137124
DescriptionALDH class 2acetaldehyde dehydrogenase 5aldehyde dehydrogenase 5aldehyde dehydrogenase X, mitochondrial
Modification date20141222
dbXrefs MIM : 100670
HGNC : HGNC
Ensembl : ENSG00000137124
HPRD : 00005
Vega : OTTHUMG00000019938
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH1B1
BioGPS: 219
Gene Expression Atlas: ENSG00000137124
The Human Protein Atlas: ENSG00000137124
PathwayNCI Pathway Interaction Database: ALDH1B1
KEGG: ALDH1B1
REACTOME: ALDH1B1
ConsensusPathDB
Pathway Commons: ALDH1B1
MetabolismMetaCyc: ALDH1B1
HUMANCyc: ALDH1B1
RegulationEnsembl's Regulation: ENSG00000137124
miRBase: chr9 :38,392,660-38,398,662
TargetScan: NM_000692
cisRED: ENSG00000137124
ContextiHOP: ALDH1B1
cancer metabolism search in PubMed: ALDH1B1
UCL Cancer Institute: ALDH1B1
Assigned class in ccmGDBC

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Phenotypic Information for ALDH1B1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH1B1
Familial Cancer Database: ALDH1B1
* 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: ALDH1B1
MedGen: ALDH1B1 (Human Medical Genetics with Condition)
ClinVar: ALDH1B1
PhenotypeMGI: ALDH1B1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH1B1

Mutations for ALDH1B1
* 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 ALDH1B1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE856261NDUFB71173191467689214677064ALDH1B117447493839630038396600
AI422203NDUFB71173191467689214677064ALDH1B117446693839630838396600

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr9:38395753-38395753p.R3H4
chr9:38395928-38395928p.T61T3
chr9:38396065-38396065p.R107L3
chr9:38396397-38396397p.A218S3
chr9:38395797-38395797p.R18S2
chr9:38395809-38395809p.A22T2
chr9:38395994-38395994p.A83A2
chr9:38396624-38396624p.I293I2
chr9:38396134-38396134p.P130H2
chr9:38396762-38396762p.T339T2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 9  3 11 821  11717
# mutation11 10  3 11 821  11817
nonsynonymous SNV 1 9  1 11 721  76 6
synonymous SNV1  1  2    1    4211
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
chr9:38395753p.R3H4
chr9:38396762p.T339T2
chr9:38395768p.R8Q2
chr9:38396569p.P130L2
chr9:38396134p.G405G2
chr9:38396624p.G275V2
chr9:38396960p.I293I2
chr9:38395964p.M1L1
chr9:38396998p.R114L1
chr9:38396249p.F485L1

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 ALDH1B1 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 ALDH1B1

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

ACTN1,ALDH1B1,CALD1,CALU,CHST3,COL8A1,DPYSL3,
FLNA,FNDC1,GLS,HEPH,MSN,MYH9,MYO1E,
NEXN,NRP2,PLS3,RAB23,RAI14,TAGLN,TIMP2
ALDH1B1,CAMK2G,CASQ2,DGKG,DMPK,FZD9,INPP5A,
ITLN1,KCNA5,LGI1,LOC401093,MT3,MUSTN1,PDE4C,
PKNOX2,POU4F1,RCAN2,TGM2,TYRP1,WFDC1,ZNF536

ALDH1B1,TMEM261,CDHR1,CDX2,DAGLA,FAM171A1,GSPT2,
IFT74,KANK1,LOC151009,MAT1A,NOTCH1,PMFBP1,PRDX5,
RGMB,SMTN,STK38L,TDGF1,TDGF1P3,TTLL11,WNK2
ALDH1B1,FAM210A,DOLK,DUSP14,ERAL1,FASTKD2,FXN,
G6PC3,GCDH,COLGALT1,H2AFY2,IPO11,NDUFAF4,NUFIP1,
OGFOD1,PROCR,RCL1,RNMTL1,SMYD5,TIMM44,TANGO6
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 ALDH1B1
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 B1approved; nutraceuticalNADH


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Cross referenced IDs for ALDH1B1
* 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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