|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LCMT2 |
Basic gene info. | Gene symbol | LCMT2 |
Gene name | leucine carboxyl methyltransferase 2 | |
Synonyms | PPM2|TYW4 | |
Cytomap | UCSC genome browser: 15q15.3 | |
Genomic location | chr15 :43619973-43622820 | |
Type of gene | protein-coding | |
RefGenes | NM_014793.4, | |
Ensembl id | ENSG00000168806 | |
Description | p21WAF1/CIP1 promoter-interacting proteintRNA wybutosine-synthesizing protein 4tRNA yW-synthesizing protein 4tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferasetRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)- | |
Modification date | 20141207 | |
dbXrefs | MIM : 611246 | |
HGNC : HGNC | ||
HPRD : 17267 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LCMT2 | |
BioGPS: 9836 | ||
Gene Expression Atlas: ENSG00000168806 | ||
The Human Protein Atlas: ENSG00000168806 | ||
Pathway | NCI Pathway Interaction Database: LCMT2 | |
KEGG: LCMT2 | ||
REACTOME: LCMT2 | ||
ConsensusPathDB | ||
Pathway Commons: LCMT2 | ||
Metabolism | MetaCyc: LCMT2 | |
HUMANCyc: LCMT2 | ||
Regulation | Ensembl's Regulation: ENSG00000168806 | |
miRBase: chr15 :43,619,973-43,622,820 | ||
TargetScan: NM_014793 | ||
cisRED: ENSG00000168806 | ||
Context | iHOP: LCMT2 | |
cancer metabolism search in PubMed: LCMT2 | ||
UCL Cancer Institute: LCMT2 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for LCMT2(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: LCMT2 |
Familial Cancer Database: LCMT2 |
* 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/ |
![]() | |
KEGG_HISTIDINE_METABOLISM KEGG_TYROSINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM |
![]() | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: LCMT2 |
MedGen: LCMT2 (Human Medical Genetics with Condition) | |
ClinVar: LCMT2 | |
Phenotype | MGI: LCMT2 (International Mouse Phenotyping Consortium) |
PhenomicDB: LCMT2 |
Mutations for LCMT2 |
* 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. |
![]() |
There's no structural variation information in COSMIC data for this gene. |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LCMT2 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 |
![]() |
Top |
![]() |
There's no copy number variation information in COSMIC data for this gene. |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=43) | (# total SNVs=10) |
![]() | ![]() |
(# total SNVs=3) | (# total SNVs=0) |
![]() |
Top |
![]() |
* 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 |
chr15:43621332-43621332 | p.F452fs*11 | 2 |
chr15:43622652-43622652 | p.A12A | 2 |
chr15:43622057-43622057 | p.P211S | 2 |
chr15:43622403-43622403 | p.L95L | 2 |
chr15:43622110-43622110 | p.Y193C | 2 |
chr15:43620879-43620879 | p.G603G | 1 |
chr15:43621681-43621681 | p.S336L | 1 |
chr15:43622516-43622516 | p.V58I | 1 |
chr15:43621302-43621302 | p.L462L | 1 |
chr15:43621889-43621889 | p.G267C | 1 |
Top |
![]() |
|
![]() |
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 | 3 |   | 3 |   |   | 5 |   | 4 |   |   | 5 | 4 |   |   | 1 |   | 9 |   | 7 |
# mutation | 2 | 5 |   | 3 |   |   | 6 |   | 4 |   |   | 6 | 4 |   |   | 1 |   | 9 |   | 9 |
nonsynonymous SNV | 2 | 5 |   | 3 |   |   | 6 |   | 3 |   |   | 5 | 2 |   |   |   |   | 6 |   | 7 |
synonymous SNV |   |   |   |   |   |   |   |   | 1 |   |   | 1 | 2 |   |   | 1 |   | 3 |   | 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]) |
Top |
![]() |
* 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 |
chr15:43621185 | p.L447I | 1 |
chr15:43622318 | p.R286W | 1 |
chr15:43621556 | p.Q73H | 1 |
chr15:43621844 | p.L444S | 1 |
chr15:43621247 | p.R285W | 1 |
chr15:43622382 | p.R64R | 1 |
chr15:43621583 | p.Q404H | 1 |
chr15:43621880 | p.E282K | 1 |
chr15:43621302 | p.V58I | 1 |
chr15:43622436 | p.G402S | 1 |
![]() |
![]() |
* 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 LCMT2 |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* 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 |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* 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 |
![]() | |||||
AAGAB,ADAL,ARPP19,FAM227B,CCNDBP1,CDAN1,COPS2, DYX1C1,FOXA1,HAUS2,FAM214A,LCMT2,LEO1,LRRC57, MFAP1,MYO5C,PIGB,BLOC1S6,SPG11,TP53BP1,ZSCAN29 | AAGAB,ATP6V1G1,RHNO1,C14orf1,C14orf169,VWA9,C3orf14, CAMK2N1,HSBP1,LCMT2,LRRC42,MYCBP,OCIAD2,PPIL1, RDH11,SNRNP40,TMEM199,TP53RK,XBP1,YIPF1,ZBTB9 | ||||
![]() | |||||
ADAL,BUB1B,KNSTRN,VWA9,EDC3,EIF3J,HAUS2, LCMT2,LRRC57,MFAP1,MRPL46,MTFMT,NDNL2,PDCD7, RPAP1,RPUSD2,RTF1,SNUPN,SPATA5L1,ZNF770,ZSCAN29 | AEN,ARID5A,ARL4C,BYSL,THEMIS2,DDX28,KIAA0040, LCMT2,MARS2,NCOA5,PDE4B,PHOSPHO1,RNF122,SERHL, SRSF2,SRSF6,SH3TC1,TRIM27,TRMT6,UTP15,ZNF131 |
![]() |
* 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 |
![]() |
Top |
Pharmacological Information for LCMT2 |
![]() |
DB Category | DB Name | DB's ID and Url link |
![]() |
* Gene Centered Interaction Network. |
![]() |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00149 | leucine carboxyl methyltransferase 2 | approved; nutraceutical | L-Leucine | ![]() | ![]() |
Top |
Cross referenced IDs for LCMT2 |
* 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 @ |