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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LPCAT3 |
Basic gene info. | Gene symbol | LPCAT3 |
Gene name | lysophosphatidylcholine acyltransferase 3 | |
Synonyms | C3F|LPCAT|LPLAT 5|LPSAT|MBOAT5|OACT5|nessy | |
Cytomap | UCSC genome browser: 12p13 | |
Genomic location | chr12 :7085346-7125842 | |
Type of gene | protein-coding | |
RefGenes | NM_005768.5, | |
Ensembl id | ENSG00000268829 | |
Description | 1-acylglycerophosphocholine O-acyltransferase1-acylglycerophosphoserine O-acyltransferaseO-acyltransferase (membrane bound) domain containing 5O-acyltransferase domain-containing protein 5lyso-PC acyltransferase 3lyso-PS acyltransferaselysophosphati | |
Modification date | 20141207 | |
dbXrefs | MIM : 611950 | |
HGNC : HGNC | ||
Ensembl : ENSG00000111684 | ||
HPRD : 12816 | ||
Vega : OTTHUMG00000168970 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LPCAT3 | |
BioGPS: 10162 | ||
Gene Expression Atlas: ENSG00000268829 | ||
The Human Protein Atlas: ENSG00000268829 | ||
Pathway | NCI Pathway Interaction Database: LPCAT3 | |
KEGG: LPCAT3 | ||
REACTOME: LPCAT3 | ||
ConsensusPathDB | ||
Pathway Commons: LPCAT3 | ||
Metabolism | MetaCyc: LPCAT3 | |
HUMANCyc: LPCAT3 | ||
Regulation | Ensembl's Regulation: ENSG00000268829 | |
miRBase: chr12 :7,085,346-7,125,842 | ||
TargetScan: NM_005768 | ||
cisRED: ENSG00000268829 | ||
Context | iHOP: LPCAT3 | |
cancer metabolism search in PubMed: LPCAT3 | ||
UCL Cancer Institute: LPCAT3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for LPCAT3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LPCAT3 |
Familial Cancer Database: LPCAT3 |
* 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_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: LPCAT3 |
MedGen: LPCAT3 (Human Medical Genetics with Condition) | |
ClinVar: LPCAT3 | |
Phenotype | MGI: LPCAT3 (International Mouse Phenotyping Consortium) |
PhenomicDB: LPCAT3 |
Mutations for LPCAT3 |
* 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 LPCAT3 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 |
AI870471 | LPCAT3 | 55 | 91 | 12 | 7125748 | 7126194 | GSG1L | 81 | 125 | 16 | 28074746 | 28304597 |
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 | 2 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=36) | (# total SNVs=4) |
(# total SNVs=0) | (# 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 |
chr12:7087511-7087511 | p.W344* | 3 |
chr12:7090313-7090313 | p.A177V | 2 |
chr12:7087832-7087832 | p.R269P | 2 |
chr12:7088678-7088678 | p.L247L | 2 |
chr12:7087528-7087528 | p.I339V | 2 |
chr12:7087581-7087581 | p.V321A | 1 |
chr12:7125611-7125611 | p.Q40* | 1 |
chr12:7090191-7090191 | p.D218Y | 1 |
chr12:7086391-7086391 | p.F461I | 1 |
chr12:7090988-7090988 | p.L148L | 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 |   | 1 |   | 1 |   |   | 1 | 1 | 3 |   |   | 2 | 2 | 2 |   |   |   | 3 |   | 7 |
# mutation |   | 1 |   | 1 |   |   | 1 | 1 | 3 |   |   | 2 | 3 | 2 |   |   |   | 3 |   | 7 |
nonsynonymous SNV |   | 1 |   | 1 |   |   |   | 1 | 2 |   |   | 1 | 3 | 2 |   |   |   | 3 |   | 7 |
synonymous SNV |   |   |   |   |   |   | 1 |   | 1 |   |   | 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 |
chr12:7087665 | p.N225S | 1 |
chr12:7091877 | p.D218Y | 1 |
chr12:7086391 | p.F461I | 1 |
chr12:7087667 | p.G214E | 1 |
chr12:7091886 | p.M436T | 1 |
chr12:7086569 | p.A177D | 1 |
chr12:7087774 | p.V391V | 1 |
chr12:7092611 | p.D161D | 1 |
chr12:7086775 | p.L381M | 1 |
chr12:7088722 | p.V157V | 1 |
Other DBs for Point Mutations |
Copy Number for LPCAT3 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 LPCAT3 |
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 |
ACSM1,ALOX15B,C15orf43,APMAP,CD9,CHRNA2,COPS7A, ISX,LPCAT3,LST-3TM12,M6PR,MPV17L,PNLIPRP3,SCP2, SERHL2,SLCO1B1,SPINK8,SRD5A1,SULT1C3,TMEM62,UGT2B28 | ABCC11,AFMID,AKR1A1,ALDH3B2,ALOX15B,GGT1,GGTLC2, HMGCS2,HRASLS2,KYNU,CERS4,LPCAT3,MPV17L,MVK, NSUN2,REEP6,SERHL2,SERHL,SPINK8,TMEM62,TMEM63C |
ACADS,ARF3,RITA1,CA13,COPS7A,DGAT1,LPCAT3, METTL7B,MLF2,OPLAH,PEBP1,PEX5,PLEKHG6,PRR13, SLC7A9,SPAM1,SPPL3,SPSB2,TMBIM6,USP5,ZNF384 | ACOX1,ANKS4B,ANO10,AP1AR,CEBPA,RHOV___CHP1,DOLPP1, ESPN,GAREM,FAM73B,GNG12,HADHA,KALRN,LPCAT3, MARVELD3,MGAT4A,MOGAT3,SEPHS2,SLC27A4,SLC41A2,SPHK2 |
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 LPCAT3 |
There's no related Drug. |
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Cross referenced IDs for LPCAT3 |
* 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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