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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ALDH4A1 |
Basic gene info. | Gene symbol | ALDH4A1 |
Gene name | aldehyde dehydrogenase 4 family, member A1 | |
Synonyms | ALDH4|P5CD|P5CDh | |
Cytomap | UCSC genome browser: 1p36 | |
Genomic location | chr1 :19197923-19217385 | |
Type of gene | protein-coding | |
RefGenes | NM_001161504.1, NM_003748.3,NM_170726.2, | |
Ensembl id | ENSG00000159423 | |
Description | L-glutamate gamma-semialdehyde dehydrogenaseP5C dehydrogenasealdehyde dehydrogenase family 4 member A1delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrialmitochondrial delta-1-pyrroline 5-carboxylate dehydrogenase | |
Modification date | 20141207 | |
dbXrefs | MIM : 606811 | |
HGNC : HGNC | ||
Ensembl : ENSG00000159423 | ||
HPRD : 06009 | ||
Vega : OTTHUMG00000002443 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ALDH4A1 | |
BioGPS: 8659 | ||
Gene Expression Atlas: ENSG00000159423 | ||
The Human Protein Atlas: ENSG00000159423 | ||
Pathway | NCI Pathway Interaction Database: ALDH4A1 | |
KEGG: ALDH4A1 | ||
REACTOME: ALDH4A1 | ||
ConsensusPathDB | ||
Pathway Commons: ALDH4A1 | ||
Metabolism | MetaCyc: ALDH4A1 | |
HUMANCyc: ALDH4A1 | ||
Regulation | Ensembl's Regulation: ENSG00000159423 | |
miRBase: chr1 :19,197,923-19,217,385 | ||
TargetScan: NM_001161504 | ||
cisRED: ENSG00000159423 | ||
Context | iHOP: ALDH4A1 | |
cancer metabolism search in PubMed: ALDH4A1 | ||
UCL Cancer Institute: ALDH4A1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for ALDH4A1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ALDH4A1 |
Familial Cancer Database: ALDH4A1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ALDH4A1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
DB320226 | PSMC5 | 1 | 181 | 17 | 61909094 | 61909379 | ALDH4A1 | 174 | 510 | 1 | 19198500 | 19198836 | |
N49444 | ALDH4A1 | 1 | 147 | 1 | 19197925 | 19198070 | RMI2 | 144 | 477 | 16 | 11445190 | 11445518 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=36) | (# total SNVs=17) |
(# total SNVs=1) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr1:19204081-19204081 | p.F322F | 4 |
chr1:19202926-19202926 | p.A407A | 3 |
chr1:19203997-19203997 | p.A350A | 3 |
chr1:19216559-19216559 | p.E35K | 3 |
chr1:19202917-19202917 | p.S410S | 2 |
chr1:19228971-19228971 | p.P16L | 2 |
chr1:19201049-19201049 | p.V496A | 2 |
chr1:19209681-19209681 | p.A205A | 2 |
chr1:19202927-19202927 | p.A407V | 2 |
chr1:19199351-19199351 | p.A560A | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   | 2 | 4 |   |   | 2 |   | 2 | 1 |   | 3 | 5 |   |   |   | 9 | 6 |   | 5 |
# mutation |   |   | 2 | 5 |   |   | 2 |   | 2 | 1 |   | 3 | 6 |   |   |   | 9 | 6 |   | 5 |
nonsynonymous SNV |   |   | 1 | 4 |   |   | 1 |   | 1 | 1 |   | 3 | 3 |   |   |   | 4 | 5 |   | 3 |
synonymous SNV |   |   | 1 | 1 |   |   | 1 |   | 1 |   |   |   | 3 |   |   |   | 5 | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr1:19204081 | p.F262F,ALDH4A1 | 5 |
chr1:19199402 | p.S483S,ALDH4A1 | 2 |
chr1:19216559 | p.E35K,ALDH4A1 | 2 |
chr1:19203721 | p.L393L,ALDH4A1 | 1 |
chr1:19209803 | p.V144M,ALDH4A1 | 1 |
chr1:19201067 | p.Q380H,ALDH4A1 | 1 |
chr1:19203948 | p.S131S,ALDH4A1 | 1 |
chr1:19209814 | p.V365M,ALDH4A1 | 1 |
chr1:19201071 | p.V128L,ALDH4A1 | 1 |
chr1:19203968 | p.A347A,ALDH4A1 | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for ALDH4A1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | aldehyde dehydrogenase 4 family, member A1 | approved; nutraceutical | NADH | ||
DB00172 | aldehyde dehydrogenase 4 family, member A1 | approved; nutraceutical | L-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 |
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