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 ALDH4A1
Basic gene info.Gene symbolALDH4A1
Gene namealdehyde dehydrogenase 4 family, member A1
SynonymsALDH4|P5CD|P5CDh
CytomapUCSC genome browser: 1p36
Genomic locationchr1 :19197923-19217385
Type of geneprotein-coding
RefGenesNM_001161504.1,
NM_003748.3,NM_170726.2,
Ensembl idENSG00000159423
DescriptionL-glutamate gamma-semialdehyde dehydrogenaseP5C dehydrogenasealdehyde dehydrogenase family 4 member A1delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrialmitochondrial delta-1-pyrroline 5-carboxylate dehydrogenase
Modification date20141207
dbXrefs MIM : 606811
HGNC : HGNC
Ensembl : ENSG00000159423
HPRD : 06009
Vega : OTTHUMG00000002443
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALDH4A1
BioGPS: 8659
Gene Expression Atlas: ENSG00000159423
The Human Protein Atlas: ENSG00000159423
PathwayNCI Pathway Interaction Database: ALDH4A1
KEGG: ALDH4A1
REACTOME: ALDH4A1
ConsensusPathDB
Pathway Commons: ALDH4A1
MetabolismMetaCyc: ALDH4A1
HUMANCyc: ALDH4A1
RegulationEnsembl's Regulation: ENSG00000159423
miRBase: chr1 :19,197,923-19,217,385
TargetScan: NM_001161504
cisRED: ENSG00000159423
ContextiHOP: ALDH4A1
cancer metabolism search in PubMed: ALDH4A1
UCL Cancer Institute: ALDH4A1
Assigned class in ccmGDBC

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Phenotypic Information for ALDH4A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALDH4A1
Familial Cancer Database: ALDH4A1
* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
KEGG_ARGININE_AND_PROLINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALDH4A1
MedGen: ALDH4A1 (Human Medical Genetics with Condition)
ClinVar: ALDH4A1
PhenotypeMGI: ALDH4A1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALDH4A1

Mutations for ALDH4A1
* 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 ALDH4A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB320226PSMC51181176190909461909379ALDH4A117451011919850019198836
N49444ALDH4A1114711919792519198070RMI2144477161144519011445518

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=17)
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
chr1:19204081-19204081p.F322F4
chr1:19216559-19216559p.E35K3
chr1:19202926-19202926p.A407A3
chr1:19203997-19203997p.A350A3
chr1:19212967-19212967p.Y96*2
chr1:19199402-19199402p.S543S2
chr1:19201947-19201947p.Y463*2
chr1:19212005-19212005p.R139C2
chr1:19202917-19202917p.S410S2
chr1:19228971-19228971p.P16L2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  24  2 21 35   96 5
# mutation  25  2 21 36   96 5
nonsynonymous SNV  14  1 11 33   45 3
synonymous SNV  11  1 1   3   51 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
chr1:19204081p.F262F,ALDH4A15
chr1:19199402p.S483S,ALDH4A12
chr1:19216559p.E35K,ALDH4A12
chr1:19201979p.S329C,ALDH4A11
chr1:19204015p.P78P,ALDH4A11
chr1:19212006p.R480C,ALDH4A11
chr1:19202827p.R307W,ALDH4A11
chr1:19204035p.I61T,ALDH4A11
chr1:19199413p.A465G,ALDH4A11
chr1:19212058p.L300P,ALDH4A11

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 ALDH4A1 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 ALDH4A1

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

ABCC11,ACSM1,ALDH3B2,ALDH4A1,ALOX15B,ARRDC1,C15orf43,
LRRC75B,CRAT,GGT1,GGT3P,GGTLC1,MMAB,MVK,
RRP7B,SERHL2,SERHL,SLCO1B1,SPINK8,SULT1C3,UGT2B28
ACTR1A,AGPAT3,ALDH4A1,ARHGAP10,BHMT2,BTBD6,DHDDS,
GPI,INPP5K,ITPK1,LEP,MAP2K1,MAP7D1,MAPKAP1,
MARCH2,MYO1C,NPLOC4,PISD,RILP,TNIP1,ZDHHC3

ALDH4A1,DPEP1,EPHB2,ETV4,F2,GPR113,GYPB,
HIST1H4G,KCNQ1,LOC151162,NKD1,OC90,OR6C68,PAH,
PLA2G4F,PMFBP1,QPRT,SNAR-F,VIL1,WDR77,ZP2
ALDH4A1,B3GNT9,CD248,CERCAM,COL1A1,COL1A2,DCLK1,
ECM1,FOXRED2,COLGALT1,IGSF1,KLHL30,LEPRE1,MFGE8,
MLLT1,NGFR,SERPINH1,SH3PXD2B,CEP41,VASH2,WTIP
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 ALDH4A1
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 4 family, member A1approved; nutraceuticalNADH
DB00172aldehyde dehydrogenase 4 family, member A1approved; nutraceuticalL-Proline


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Cross referenced IDs for ALDH4A1
* 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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