|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AGPAT1 |
Basic gene info. | Gene symbol | AGPAT1 |
Gene name | 1-acylglycerol-3-phosphate O-acyltransferase 1 | |
Synonyms | 1-AGPAT1|G15|LPAAT-alpha|LPAATA | |
Cytomap | UCSC genome browser: 6p21.3 | |
Genomic location | chr6 :32135982-32143916 | |
Type of gene | protein-coding | |
RefGenes | NM_006411.3, NM_032741.4, | |
Ensembl id | ENSG00000204310 | |
Description | 1-AGP acyltransferase 11-AGPAT 11-acyl-sn-glycerol-3-phosphate acyltransferase alpha1-acylglycerol-3-phosphate O-acyltransferase 1 (acetoacetly Coenzyme A thiolase)1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, | |
Modification date | 20141207 | |
dbXrefs | MIM : 603099 | |
HGNC : HGNC | ||
Ensembl : ENSG00000204310 | ||
HPRD : 04372 | ||
Vega : OTTHUMG00000031210 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_AGPAT1 | |
BioGPS: 10554 | ||
Gene Expression Atlas: ENSG00000204310 | ||
The Human Protein Atlas: ENSG00000204310 | ||
Pathway | NCI Pathway Interaction Database: AGPAT1 | |
KEGG: AGPAT1 | ||
REACTOME: AGPAT1 | ||
ConsensusPathDB | ||
Pathway Commons: AGPAT1 | ||
Metabolism | MetaCyc: AGPAT1 | |
HUMANCyc: AGPAT1 | ||
Regulation | Ensembl's Regulation: ENSG00000204310 | |
miRBase: chr6 :32,135,982-32,143,916 | ||
TargetScan: NM_006411 | ||
cisRED: ENSG00000204310 | ||
Context | iHOP: AGPAT1 | |
cancer metabolism search in PubMed: AGPAT1 | ||
UCL Cancer Institute: AGPAT1 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for AGPAT1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AGPAT1 |
Familial Cancer Database: AGPAT1 |
* 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_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: AGPAT1 |
MedGen: AGPAT1 (Human Medical Genetics with Condition) | |
ClinVar: AGPAT1 | |
Phenotype | MGI: AGPAT1 (International Mouse Phenotyping Consortium) |
PhenomicDB: AGPAT1 |
Mutations for AGPAT1 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | AGPAT1 | chr6 | 32138091 | 32138491 | chr6 | 32230385 | 32230785 | |
pancreas | AGPAT1 | chr6 | 32141162 | 32141182 | AGPAT1 | chr6 | 32136603 | 32136623 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AGPAT1 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 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=18) | (# total SNVs=6) |
(# total SNVs=1) | (# total SNVs=0) |
Top |
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 |
chr6:32137188-32137188 | p.T239T | 3 |
chr6:32138354-32138354 | p.R120C | 2 |
chr6:32139093-32139093 | p.R61C | 2 |
chr6:32138256-32138256 | p.T152T | 1 |
chr6:32139159-32139159 | p.A39fs*28 | 1 |
chr6:32137189-32137189 | p.T239M | 1 |
chr6:32138260-32138260 | p.R151L | 1 |
chr6:32139185-32139185 | p.P30L | 1 |
chr6:32137210-32137210 | p.R232Q | 1 |
chr6:32139205-32139205 | p.P23P | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   |   | 1 | 5 | 2 |   | 3 |   |   |   |   | 5 | 2 |   |   |   | 4 | 4 |   |   |
# mutation |   |   | 1 | 5 | 2 |   | 3 |   |   |   |   | 7 | 2 |   |   |   | 4 | 4 |   |   |
nonsynonymous SNV |   |   |   | 3 | 2 |   | 2 |   |   |   |   | 7 |   |   |   |   | 2 | 3 |   |   |
synonymous SNV |   |   | 1 | 2 |   |   | 1 |   |   |   |   |   | 2 |   |   |   | 2 | 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]) |
Top |
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 |
chr6:32137188 | p.T239T,AGPAT1 | 3 |
chr6:32138807 | p.G81W,AGPAT1 | 2 |
chr6:32138354 | p.S211S,AGPAT1 | 1 |
chr6:32137210 | p.I208V,AGPAT1 | 1 |
chr6:32138714 | p.G185A,AGPAT1 | 1 |
chr6:32137211 | p.V158V,AGPAT1 | 1 |
chr6:32138728 | p.T152T,AGPAT1 | 1 |
chr6:32137758 | p.X284X,AGPAT1 | 1 |
chr6:32138758 | p.R151L,AGPAT1 | 1 |
chr6:32137054 | p.G283V,AGPAT1 | 1 |
Other DBs for Point Mutations |
Copy Number for AGPAT1 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] |
Top |
Gene Expression for AGPAT1 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
ABCF1,AGPAT1,BAG6,GPANK1,C6orf106,CSNK2B,CUTA, DHX16,EHMT2,FKBPL,GNL1,GTF2H4,LEMD2,LSM2, PBX2,NELFE,RNF5,RXRB,SKIV2L,TRIM27,VARS | ABHD14A,AGPAT1,ATP6V1F,WDR83OS,COMMD9,COPS7A,DYNLRB1, ERI3,FAM127A,FAM96B,HCFC1R1,HIGD2A,OST4,PSMB4, PSMF1,RNASEK,SCNM1,SLC35A4,UBL7,VKORC1,ZNF358 |
AGPAT1,PRRC2A,BAG6,BRPF3,MIR99AHG,C6orf106,C6orf89, CUL7,FAM168A,FRY,ITPKB,LATS2,PBX2,SAMD14, SH3BP5L,SHC1,TLN1,ZBTB22,ZFAND3,ZMIZ1,ZKSCAN8 | ABCD1,ACOX2,AGPAT1,AQP1,CDIPT,DBP,DEFB131, EEPD1,MAOB,NPC1L1,PAQR7,PDK2,PLOD1,PPP2R5D, RAB11FIP3,SEMA6C,TBC1D13,TMEM198,TMEM25,VPS26B,ZNF358 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for AGPAT1 |
There's no related Drug. |
Top |
Cross referenced IDs for AGPAT1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |