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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ALDH1A1 |
Basic gene info. | Gene symbol | ALDH1A1 |
Gene name | aldehyde dehydrogenase 1 family, member A1 | |
Synonyms | ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1 | |
Cytomap | UCSC genome browser: 9q21.13 | |
Genomic location | chr9 :75515577-75568233 | |
Type of gene | protein-coding | |
RefGenes | NM_000689.4, | |
Ensembl id | ENSG00000165092 | |
Description | ALDH class 1ALHDIIRALDH 1acetaldehyde dehydrogenase 1aldehyde dehydrogenase 1, solublealdehyde dehydrogenase, liver cytosolicepididymis luminal protein 12epididymis luminal protein 9epididymis secretory sperm binding protein Li 53eretinal dehydro | |
Modification date | 20141222 | |
dbXrefs | MIM : 100640 | |
HGNC : HGNC | ||
Ensembl : ENSG00000165092 | ||
HPRD : 00001 | ||
Vega : OTTHUMG00000020019 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ALDH1A1 | |
BioGPS: 216 | ||
Gene Expression Atlas: ENSG00000165092 | ||
The Human Protein Atlas: ENSG00000165092 | ||
Pathway | NCI Pathway Interaction Database: ALDH1A1 | |
KEGG: ALDH1A1 | ||
REACTOME: ALDH1A1 | ||
ConsensusPathDB | ||
Pathway Commons: ALDH1A1 | ||
Metabolism | MetaCyc: ALDH1A1 | |
HUMANCyc: ALDH1A1 | ||
Regulation | Ensembl's Regulation: ENSG00000165092 | |
miRBase: chr9 :75,515,577-75,568,233 | ||
TargetScan: NM_000689 | ||
cisRED: ENSG00000165092 | ||
Context | iHOP: ALDH1A1 | |
cancer metabolism search in PubMed: ALDH1A1 | ||
UCL Cancer Institute: ALDH1A1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for ALDH1A1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ALDH1A1 |
Familial Cancer Database: ALDH1A1 |
* This gene is included in those cancer gene databases. |
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_RETINOL_METABOLISM |
Mutations for ALDH1A1 |
* 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 ALDH1A1 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 |
DA668305 | HSPA8 | 2 | 89 | 11 | 122930043 | 122930129 | ALDH1A1 | 90 | 558 | 9 | 75531952 | 75542085 | |
BF436998 | ALDH1A1 | 35 | 274 | 9 | 75515618 | 75515857 | EPB41L4A | 273 | 330 | 5 | 111754705 | 111754762 | |
AI493829 | ALDH1A1 | 1 | 21 | 9 | 75652605 | 75652625 | ELL | 8 | 477 | 19 | 18555203 | 18555674 | |
AA515000 | ALDH1A1 | 8 | 87 | 9 | 75515725 | 75515804 | ALDH1A1 | 81 | 217 | 9 | 75515589 | 75515725 | |
BQ317586 | ALDH1A1 | 23 | 244 | 9 | 75540456 | 75543894 | ALDH1A1 | 238 | 333 | 9 | 75545800 | 75545895 | |
BU674486 | ALDH1A1 | 19 | 132 | 9 | 75515585 | 75515698 | ALDH1A1 | 122 | 538 | 9 | 75515748 | 75516164 | |
DA896624 | ALDH1A1 | 1 | 475 | 9 | 75531935 | 75567934 | ALDH1A1 | 469 | 540 | 9 | 75540406 | 75540477 | |
BU685483 | ALDH1A1 | 18 | 129 | 9 | 75515587 | 75515698 | ALDH1A1 | 119 | 577 | 9 | 75515706 | 75516164 |
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=44) | (# total SNVs=16) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr9:75539039-75539039 | p.P215S | 3 |
chr9:75520915-75520915 | p.C464C | 2 |
chr9:75520934-75520934 | p.G458D | 2 |
chr9:75545879-75545879 | p.P76P | 2 |
chr9:75516128-75516128 | p.S501L | 1 |
chr9:75531961-75531961 | p.I304V | 1 |
chr9:75545818-75545818 | p.E97K | 1 |
chr9:75524601-75524601 | p.F425L | 1 |
chr9:75539031-75539031 | p.G217G | 1 |
chr9:75555088-75555088 | p.L49L | 1 |
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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 | 4 | 6 |   | 10 | 1 |   | 1 |   | 3 |   |   | 5 | 1 | 3 |   |   | 3 | 6 |   | 9 |
# mutation | 4 | 6 |   | 10 | 1 |   | 1 |   | 3 |   |   | 5 | 1 | 3 |   |   | 3 | 6 |   | 10 |
nonsynonymous SNV | 2 | 2 |   | 9 | 1 |   |   |   | 1 |   |   | 4 |   |   |   |   | 3 | 2 |   | 8 |
synonymous SNV | 2 | 4 |   | 1 |   |   | 1 |   | 2 |   |   | 1 | 1 | 3 |   |   |   | 4 |   | 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 |
chr9:75516128 | p.W375S | 1 |
chr9:75539031 | p.A258S | 1 |
chr9:75526890 | p.P76P | 1 |
chr9:75545795 | p.S501L | 1 |
chr9:75531955 | p.A366A | 1 |
chr9:75516163 | p.G217G | 1 |
chr9:75540461 | p.D56N | 1 |
chr9:75526929 | p.V489V | 1 |
chr9:75545819 | p.G365R | 1 |
chr9:75531961 | p.V191A | 1 |
Other DBs for Point Mutations |
Copy Number for ALDH1A1 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 ALDH1A1 |
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 |
ABCA6,ABCA9,ALDH1A1,C10orf128,CCDC80,CHRDL1,CLEC1A, DOCK11,FLI1,FREM1,GIMAP6,GIMAP8,HTR2B,IGF1, KCNS2,KCTD12,LHFP,MFAP4,PDE1A,SLC9A9,ZEB2 | ALDH1A1,CHRDL1,CREBL2,DIRC3,ECM2,GTDC1,HNMT, ITGB1,MAN1A1,NEK7,OSTM1,PALM2-AKAP2,PGRMC2,PTPRQ, RGS22,SEPT11,SERINC1,SH3D19,TIMP3,VAMP3,VGLL3 | ||||
ABCB6,ALDH1A1,COLCA1,FAM222A,LINC00261,CA8,CACNA1B, CALML6,CDK6,HPCAL1,HPN,HS3ST5,IGF2-AS,IFNL2, INS,JPH1,KIAA1324,LIN7A,LOC100128675,SOX2,TRIM71 | ALDH1A1,ANO6,AQP1,C4orf3,CYP2U1,FAM172A,GRIK2, IMMP2L,ISCU,KCTD3,LMO4,PFN2,CPQ,PLA2G4C, SEC22C,STK33,TMEM64,VKORC1,WRB,ZNF16,ZNF639 |
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 ALDH1A1 |
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 1 family, member A1 | approved; nutraceutical | NADH | ||
DB00162 | aldehyde dehydrogenase 1 family, member A1 | approved; nutraceutical | Vitamin A | ||
DB00755 | aldehyde dehydrogenase 1 family, member A1 | approved; nutraceutical; investigational | Tretinoin | ||
DB01907 | aldehyde dehydrogenase 1 family, member A1 | experimental | Nicotinamide-Adenine-Dinucleotide | ||
DB04447 | aldehyde dehydrogenase 1 family, member A1 | experimental | 1,4-Dithiothreitol | ||
DB00958 | aldehyde dehydrogenase 1 family, member A1 | approved | Carboplatin | ||
DB04572 | aldehyde dehydrogenase 1 family, member A1 | approved | Thiotepa | ||
DB00531 | aldehyde dehydrogenase 1 family, member A1 | approved; investigational | Cyclophosphamide |
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Cross referenced IDs for ALDH1A1 |
* 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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