Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 TRDMT1
Basic gene info.Gene symbolTRDMT1
Gene nametRNA aspartic acid methyltransferase 1
SynonymsDMNT2|DNMT2|MHSAIIP|PUMET|RNMT1
CytomapUCSC genome browser: 10p15.1
Genomic locationchr10 :17184981-17244070
Type of geneprotein-coding
RefGenesNM_004412.5,
NM_176081.2,NM_176083.2,NM_176084.1,NM_176085.1,
NM_176086.1,
Ensembl idENSG00000107614
DescriptionDNA (cytosine-5)-methyltransferase-like protein 2DNA MTase homolog HsaIIPDNA methyltransferase-2tRNA (cytosine(38)-C(5))-methyltransferasetRNA (cytosine-5-)-methyltransferase
Modification date20141207
dbXrefs MIM : 602478
HGNC : HGNC
HPRD : 16001
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TRDMT1
BioGPS: 1787
Gene Expression Atlas: ENSG00000107614
The Human Protein Atlas: ENSG00000107614
PathwayNCI Pathway Interaction Database: TRDMT1
KEGG: TRDMT1
REACTOME: TRDMT1
ConsensusPathDB
Pathway Commons: TRDMT1
MetabolismMetaCyc: TRDMT1
HUMANCyc: TRDMT1
RegulationEnsembl's Regulation: ENSG00000107614
miRBase: chr10 :17,184,981-17,244,070
TargetScan: NM_004412
cisRED: ENSG00000107614
ContextiHOP: TRDMT1
cancer metabolism search in PubMed: TRDMT1
UCL Cancer Institute: TRDMT1
Assigned class in ccmGDBC

Top
Phenotypic Information for TRDMT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TRDMT1
Familial Cancer Database: TRDMT1
* 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_CYSTEINE_AND_METHIONINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TRDMT1
MedGen: TRDMT1 (Human Medical Genetics with Condition)
ClinVar: TRDMT1
PhenotypeMGI: TRDMT1 (International Mouse Phenotyping Consortium)
PhenomicDB: TRDMT1

Mutations for TRDMT1
* 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
ovaryTRDMT1chr101723330517233325CUBNchr101714416617144186
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 TRDMT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA483206TRDMT11514101719550617199765NID2514839145248580652486897
BF825680TRDMT116264101718578317186032PANK1256339109134409391344176
BF827370TRDMT122271101718578317186032PANK1263346109134409391344176
BF827371TRDMT17256101718578317186032PANK1248331109134409391344176
BF827381TRDMT114259101718578317186032PANK1251334109134409391344176
BF827382TRDMT13252101718578317186032PANK1244327109134409391344176

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr10:17199651-17199651p.D226H4
chr10:17216556-17216556p.T56T3
chr10:17201225-17201225p.G155S3
chr10:17199558-17199558p.L257V2
chr10:17210904-17210904p.E63K2
chr10:17204187-17204187p.H101Y2
chr10:17191103-17191103p.R371H2
chr10:17199528-17199528p.L267I1
chr10:17210875-17210875p.M72I1
chr10:17199723-17199723p.E202Q1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 7  1 3  3 3 1 5 7
# mutation21 7  1 3  3 3 1 5 7
nonsynonymous SNV21 6  1 2  3 2   5 7
synonymous SNV   1    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])

Top
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
chr10:17199651p.D226Y2
chr10:17199740p.Q328H1
chr10:17216575p.E172A1
chr10:17199442p.Y320C1
chr10:17201171p.R162L1
chr10:17191103p.E317D1
chr10:17216603p.G155V1
chr10:17199454p.V314A1
chr10:17201173p.G155S1
chr10:17191129p.K295N1

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 TRDMT1 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 TRDMT1

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

: Open all plots for all cancer types


Top
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

ABI1,ARHGAP21,ARL5B,CCDC82,CCNY,FAM171A1,GDI2,
GTPBP4,JRKL,KCNQ4,MAML2,MLLT10,MTMR2,NMT2,
PRTFDC1,RSU1,STAM,SUV39H2,TRDMT1,USP6NL,ZNF462
ACAP2,ANKRD13C,ATP11C,BNIP2,C16orf52,CCDC82,DCUN1D4,
DIS3,EXOC1,GABPA,KIAA1033,NR2C1,OSBPL8,PJA2,
BLOC1S6,PRKD3,RAB11FIP2,SEPT10,SSFA2,TRDMT1,ZDHHC17

ATP5C1,C12orf29,MZT1,CCDC59,CCT4,CDC123,COMMD3,
COMMD8,CUL2,FAM188A,GDI2,HSPA14,N6AMT2,RSL24D1,
SEPHS1,SRSF3,STAM,TRDMT1,YEATS4,YWHAQ,ZFAND1
ANAPC16,SMIM20,CDKN2AIPNL,GLO1,GNPAT,GOLGA7,IKZF5,
LIPT1,MBIP,CMC4,PRKAG2,RARS2,RBBP9,SMYD2,
TADA1,TMEM14A,TMEM18,TRDMT1,TRMT61B,ZNF565,ZNF620
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for TRDMT1
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
DB00738tRNA aspartic acid methyltransferase 1approvedPentamidine
DB01752tRNA aspartic acid methyltransferase 1experimentalS-Adenosyl-L-Homocysteine
DB04077tRNA aspartic acid methyltransferase 1experimentalGlycerol


Top
Cross referenced IDs for TRDMT1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas