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 ALDH7A1
Basic gene info.Gene symbolALDH7A1
Gene namealdehyde dehydrogenase 7 family, member A1
SynonymsATQ1|EPD|PDE
CytomapUCSC genome browser: 5q31
Genomic locationchr5 :125877532-125931082
Type of geneprotein-coding
RefGenesNM_001182.4,
NM_001201377.1,NM_001202404.1,
Ensembl idENSG00000164904
Description26g turgor protein homologP6c dehydrogenasealpha-AASA dehydrogenasealpha-aminoadipic semialdehyde dehydrogenaseantiquitin-1betaine aldehyde dehydrogenasedelta1-piperideine-6-carboxylate dehydrogenase
Modification date20141219
dbXrefs MIM : 107323
HGNC : HGNC
Ensembl : ENSG00000164904
HPRD : 00124
Vega : OTTHUMG00000128942
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH7A1
BioGPS: 501
Gene Expression Atlas: ENSG00000164904
The Human Protein Atlas: ENSG00000164904
PathwayNCI Pathway Interaction Database: ALDH7A1
KEGG: ALDH7A1
REACTOME: ALDH7A1
ConsensusPathDB
Pathway Commons: ALDH7A1
MetabolismMetaCyc: ALDH7A1
HUMANCyc: ALDH7A1
RegulationEnsembl's Regulation: ENSG00000164904
miRBase: chr5 :125,877,532-125,931,082
TargetScan: NM_001182
cisRED: ENSG00000164904
ContextiHOP: ALDH7A1
cancer metabolism search in PubMed: ALDH7A1
UCL Cancer Institute: ALDH7A1
Assigned class in ccmGDBC

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Phenotypic Information for ALDH7A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH7A1
Familial Cancer Database: ALDH7A1
* 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
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALDH7A1
MedGen: ALDH7A1 (Human Medical Genetics with Condition)
ClinVar: ALDH7A1
PhenotypeMGI: ALDH7A1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH7A1

Mutations for ALDH7A1
* 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
ovaryALDH7A1chr5125879283125879303ALDH7A1chr5125883820125883840
prostateALDH7A1chr5125897310125899310chr193195051331952513
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 ALDH7A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ649564ALDH7A114835125918562125930875MRPS1547855313692137236921447
BF821670ALDH7A11281835125900813125900868MALAT1182483116526782265268123
AA165440ALDH7A114255125880448125885898UBAP141854793422450734224641
BG434132LOC1005058762323723742684537428837ALDH7A12246475125899506125899926

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                1
GAIN (# sample)                 
LOSS (# sample)                1
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=23)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr5:125912844-125912844p.A165T2
chr5:125930689-125930689p.?2
chr5:125887819-125887819p.R376H2
chr5:125930750-125930750p.L19L2
chr5:125887820-125887820p.R376C2
chr5:125903997-125903997p.S247S1
chr5:125885926-125885926p.I431M1
chr5:125919662-125919662p.D91N1
chr5:125891653-125891653p.A327T1
chr5:125904008-125904008p.F244L1

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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
# sample   12  2    431  113 3
# mutation   11  2    431  103 3
nonsynonymous SNV   7  2    311  93 2
synonymous SNV   4       12   1  1
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
chr5:125887819p.R367C,ALDH7A12
chr5:125887820p.A305A,ALDH7A12
chr5:125895025p.A305S,ALDH7A12
chr5:125896775p.R367H,ALDH7A12
chr5:125912887p.N205K,ALDH7A11
chr5:125887732p.A355T,ALDH7A11
chr5:125896802p.I190F,ALDH7A11
chr5:125918566p.V346A,ALDH7A11
chr5:125887746p.L178L,ALDH7A11
chr5:125896808p.A333A,ALDH7A11

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 ALDH7A1 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 ALDH7A1

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

AACS,ALDH7A1,ALOX15B,ATP13A4,C15orf43,CLDN8,CTNNBIP1,
DBI,FKBP5,GRAMD3,HIBCH,MCCC1,MVK,OXER1,
SAMM50,SCP2,SERHL2,SLCO1B1,SRP19,UGT2B28,WLS
AHCY,ALDH7A1,ASTN2,C1orf226,CHRNB2,EDN3,EMILIN3,
FZD1,GNG7,HS6ST2,KIAA1324,LPAR3,LZTS1,NIPSNAP1,
NOS1AP,PSRC1,PTK7,SMPDL3B,ST8SIA2,TRIM9,UTP14A

AADAT,ACAT1,ALDH2,ALDH7A1,LINC01184,HARS2,HSD17B4,
IDH1,LMNB1,MCCC2,ME3,MRPS27,NFIA,NLN,
PHAX,QDPR,RIOK2,SAMM50,SETMAR,SLC12A2,VWA2
ALDH6A1,ALDH7A1,ARL6IP1,APMAP,FGGY,GJB1,HADH,
HSDL2,IGFBP2,LRPPRC,MCCC1,MIPEP,MLYCD,PCCA,
ECI2,PHKB,RPUSD2,RRM2B,SUCLG2,THNSL1,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 ALDH7A1
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 7 family, member A1approved; nutraceuticalNADH
DB00165aldehyde dehydrogenase 7 family, member A1approved; nutraceuticalPyridoxine
DB00515aldehyde dehydrogenase 7 family, member A1approvedCisplatin


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Cross referenced IDs for ALDH7A1
* 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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