Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for LCMT1
Basic gene info.Gene symbolLCMT1
Gene nameleucine carboxyl methyltransferase 1
SynonymsLCMT|PPMT1
CytomapUCSC genome browser: 16p12.1
Genomic locationchr16 :25123046-25189551
Type of geneprotein-coding
RefGenesNM_001032391.1,
NM_016309.2,
Ensembl idENSG00000205629
Description[Phosphatase 2A protein]-leucine-carboxy methyltransferase 1protein phosphatase methyltransferase 1protein-leucine O-methyltransferase
Modification date20141207
dbXrefs MIM : 610286
HGNC : HGNC
Ensembl : ENSG00000205629
HPRD : 17266
Vega : OTTHUMG00000177182
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LCMT1
BioGPS: 51451
Gene Expression Atlas: ENSG00000205629
The Human Protein Atlas: ENSG00000205629
PathwayNCI Pathway Interaction Database: LCMT1
KEGG: LCMT1
REACTOME: LCMT1
ConsensusPathDB
Pathway Commons: LCMT1
MetabolismMetaCyc: LCMT1
HUMANCyc: LCMT1
RegulationEnsembl's Regulation: ENSG00000205629
miRBase: chr16 :25,123,046-25,189,551
TargetScan: NM_001032391
cisRED: ENSG00000205629
ContextiHOP: LCMT1
cancer metabolism search in PubMed: LCMT1
UCL Cancer Institute: LCMT1
Assigned class in ccmGDBC

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Phenotypic Information for LCMT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LCMT1
Familial Cancer Database: LCMT1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_HISTIDINE_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LCMT1
MedGen: LCMT1 (Human Medical Genetics with Condition)
ClinVar: LCMT1
PhenotypeMGI: LCMT1 (International Mouse Phenotyping Consortium)
PhenomicDB: LCMT1

Mutations for LCMT1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasLCMT1chr162517242925172449chr162520177825201798
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LCMT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1       1 1     1
GAIN (# sample)1       1       1
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=0

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  241 1 1  81   4213
# mutation  241 1 1  81   4213
nonsynonymous SNV  241 1 1  61   2212
synonymous SNV           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])

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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr16:25123230p.L140L,LCMT11
chr16:25151534p.S9C,LCMT11
chr16:25176022p.E143Q,LCMT11
chr16:25123281p.V26A,LCMT11
chr16:25162930p.P151A,LCMT11
chr16:25180479p.Q52P,LCMT11
chr16:25139837p.S154S,LCMT11
chr16:25172470p.G69V,LCMT11
chr16:25180501p.A155T,LCMT11
chr16:25143723p.R73Q,LCMT11

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for LCMT1 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 LCMT1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

BCKDK,CCDC101,CD2BP2,ECI1,FAHD1,GFER,JMJD8,
LCMT1,ZNF205-AS1,MLST8,KAT8,NDUFAB1,NDUFB10,NSMCE1,
NUDT16L1,PHKG2,POLR3K,PPP4C,SNRNP25,TMEM186,TUFM
PTRHD1,CUTA,DCTPP1,DDX28,DIABLO,DNTTIP1,EXOSC7,
GEMIN7,HDAC3,LCMT1,NHP2,NHP2L1,NPM3,OTUB1,
PRCC,PRMT1,RPL13A,RPLP1,SNRPD2,TMEM134,UBAC2

BCL7C,BOLA2,FOPNL,WDR83OS,CCDC101,COX4I1,DNAJC19,
FAM192A,INO80E,LCMT1,NDUFAB1,NSMCE1,NUTF2,PPP4C,
RPS15A,RSL1D1,THOC7,THYN1,TMEM219,TUFM,ZNHIT1
APPL2,B3GNT8,KDF1,C1orf210,CHMP2A,CLDN7,DAZAP2,
GPBP1L1,HHLA2,IFNGR2,IL10RB,IST1,LCMT1,MARVELD3,
P2RX4,PPARG,PRR15,SLC35D2,TMEM170A,TMEM45B,TMPRSS4
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for LCMT1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00149leucine carboxyl methyltransferase 1approved; nutraceuticalL-Leucine


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Cross referenced IDs for LCMT1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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