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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AGPAT4 |
Basic gene info. | Gene symbol | AGPAT4 |
Gene name | 1-acylglycerol-3-phosphate O-acyltransferase 4 | |
Synonyms | 1-AGPAT4|LPAAT-delta|dJ473J16.2 | |
Cytomap | UCSC genome browser: 6q26 | |
Genomic location | chr6 :161551056-161695107 | |
Type of gene | protein-coding | |
RefGenes | NM_020133.2, NM_001012733.1,NM_001012734.1, | |
Ensembl id | ENSG00000026652 | |
Description | 1-AGP acyltransferase 41-AGPAT 41-acyl-sn-glycerol-3-phosphate acyltransferase delta1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)lysophosphatidic acid acyltransferase deltalysophosphatidic acid acyltran | |
Modification date | 20141207 | |
dbXrefs | MIM : 614795 | |
HGNC : HGNC | ||
Ensembl : ENSG00000026652 | ||
HPRD : 12437 | ||
Vega : OTTHUMG00000015966 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_AGPAT4 | |
BioGPS: 56895 | ||
Gene Expression Atlas: ENSG00000026652 | ||
The Human Protein Atlas: ENSG00000026652 | ||
Pathway | NCI Pathway Interaction Database: AGPAT4 | |
KEGG: AGPAT4 | ||
REACTOME: AGPAT4 | ||
ConsensusPathDB | ||
Pathway Commons: AGPAT4 | ||
Metabolism | MetaCyc: AGPAT4 | |
HUMANCyc: AGPAT4 | ||
Regulation | Ensembl's Regulation: ENSG00000026652 | |
miRBase: chr6 :161,551,056-161,695,107 | ||
TargetScan: NM_020133 | ||
cisRED: ENSG00000026652 | ||
Context | iHOP: AGPAT4 | |
cancer metabolism search in PubMed: AGPAT4 | ||
UCL Cancer Institute: AGPAT4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for AGPAT4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AGPAT4 |
Familial Cancer Database: AGPAT4 |
* 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_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: AGPAT4 |
MedGen: AGPAT4 (Human Medical Genetics with Condition) | |
ClinVar: AGPAT4 | |
Phenotype | MGI: AGPAT4 (International Mouse Phenotyping Consortium) |
PhenomicDB: AGPAT4 |
Mutations for AGPAT4 |
* 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 | AGPAT4 | chr6 | 161570444 | 161570444 | AGPAT4 | chr6 | 161575006 | 161575006 |
pancreas | AGPAT4 | chr6 | 161639743 | 161639763 | AGPAT4 | chr6 | 161639797 | 161639817 |
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 AGPAT4 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 |
DA282561 | PDE4D | 1 | 100 | 5 | 59129537 | 59129636 | AGPAT4 | 101 | 575 | 6 | 161587303 | 161695030 | |
BU073418 | AGPAT4 | 1 | 258 | 6 | 161551572 | 161551829 | AGPAT4 | 259 | 459 | 6 | 161551334 | 161551534 | |
BU071898 | AGPAT4 | 8 | 224 | 6 | 161551334 | 161551550 | AGPAT4 | 225 | 434 | 6 | 161551572 | 161551781 | |
BU947826 | AGPAT4 | 8 | 224 | 6 | 161551334 | 161551550 | AGPAT4 | 225 | 428 | 6 | 161551572 | 161551775 | |
AK126043 | AGPAT4 | 1 | 719 | 6 | 161564416 | 161565134 | C12orf65 | 713 | 4316 | 12 | 123732823 | 123738503 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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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=34) | (# total SNVs=15) |
(# total SNVs=2) | (# 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 |
chr6:161574408-161574408 | p.A212T | 3 |
chr6:161560485-161560485 | p.T337T | 3 |
chr6:161560462-161560462 | p.F345Y | 2 |
chr6:161653200-161653200 | p.V16F | 2 |
chr6:161557582-161557582 | p.L376R | 2 |
chr6:161560586-161560586 | p.R304W | 2 |
chr6:161560589-161560589 | p.R303fs*7 | 2 |
chr6:161575237-161575237 | p.R152C | 2 |
chr6:161575278-161575278 | p.F138S | 1 |
chr6:161587397-161587397 | p.T77T | 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 |   | 2 |   | 11 | 1 |   | 2 |   |   |   |   | 8 | 5 | 2 |   |   | 5 | 6 |   | 7 |
# mutation |   | 2 |   | 10 | 1 |   | 2 |   |   |   |   | 9 | 5 | 2 |   |   | 4 | 7 |   | 6 |
nonsynonymous SNV |   | 2 |   | 7 |   |   | 2 |   |   |   |   | 7 | 1 | 2 |   |   | 3 | 5 |   | 5 |
synonymous SNV |   |   |   | 3 | 1 |   |   |   |   |   |   | 2 | 4 |   |   |   | 1 | 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]) |
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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 |
chr6:161560485 | p.T337T | 3 |
chr6:161574408 | p.A212T | 3 |
chr6:161557582 | p.R152C | 2 |
chr6:161575237 | p.L376R | 2 |
chr6:161587376 | p.R179Q | 1 |
chr6:161574397 | p.K84K | 1 |
chr6:161575274 | p.K168T | 1 |
chr6:161587387 | p.A81T | 1 |
chr6:161560486 | p.T337M | 1 |
chr6:161575278 | p.H161Y | 1 |
Other DBs for Point Mutations |
Copy Number for AGPAT4 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 AGPAT4 |
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 |
AGPAT4,AGPAT4-IT1,CENPW,CLIP2,FBLIM1,FHL3,GPX7, HYMAI,ITPRIP,KCNMB2,LIX1L,MAP4K4,MFAP2,NRN1, NXN,PIK3CA,PLEKHG2,SERPINH1,SH3PXD2B,TUBB6,VIM | AGPAT4,ATP8B2,C14orf132,KIAA0930,COL1A2,CPZ,DZIP1, FAM46A,FOXF2,GLG1,GLI2,ISLR,JAM3,MYO1E, PAPLN,PRTFDC1,PTGFRN,PXN,THBS2,THBS3,TRAM2 |
AGPAT4,AHDC1,AHNAK,B3GNT9,BASP1,AGPAT4-IT1,CCDC88A, CYTH1,IRAK3,KLC1,KLF9,LOXL1,MMP2,MOB3A, NLGN2,PEAR1,PIP5K1C,PLXDC2,SPSB4,ST5,SWAP70 | ACTB,ACVR1,ADARB1,AGPAT4,AHNAK2,DYSF,EHBP1L1, FBXO32,FRMPD4,GNAO1,MAP7D1,MICALL1,NRG2,NRP2, TENM3___TENM1,OLFML2A,PCDH7,PNMA1,SDC3,TBC1D1,TFE3 |
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 AGPAT4 |
There's no related Drug. |
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Cross referenced IDs for AGPAT4 |
* 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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