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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TMLHE |
Basic gene info. | Gene symbol | TMLHE |
Gene name | trimethyllysine hydroxylase, epsilon | |
Synonyms | AUTSX6|BBOX2|TMLD|TMLH|TMLHED|XAP130 | |
Cytomap | UCSC genome browser: Xq28 | |
Genomic location | chrX :154722195-154842622 | |
Type of gene | protein-coding | |
RefGenes | NM_001184797.1, NM_018196.3, | |
Ensembl id | ENSG00000267946 | |
Description | TML hydroxylaseTML-alpha-ketoglutarate dioxygenasebutyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2epsilon-trimethyllysine 2-oxoglutarate dioxygenaseepsilon-trimethyllysine hydroxylasetrimethyllysine dioxygenase, m | |
Modification date | 20141207 | |
dbXrefs | MIM : 300777 | |
HGNC : HGNC | ||
Ensembl : ENSG00000185973 | ||
HPRD : 06743 | ||
Vega : OTTHUMG00000022674 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TMLHE | |
BioGPS: 55217 | ||
Gene Expression Atlas: ENSG00000267946 | ||
The Human Protein Atlas: ENSG00000267946 | ||
Pathway | NCI Pathway Interaction Database: TMLHE | |
KEGG: TMLHE | ||
REACTOME: TMLHE | ||
ConsensusPathDB | ||
Pathway Commons: TMLHE | ||
Metabolism | MetaCyc: TMLHE | |
HUMANCyc: TMLHE | ||
Regulation | Ensembl's Regulation: ENSG00000267946 | |
miRBase: chrX :154,722,195-154,842,622 | ||
TargetScan: NM_001184797 | ||
cisRED: ENSG00000267946 | ||
Context | iHOP: TMLHE | |
cancer metabolism search in PubMed: TMLHE | ||
UCL Cancer Institute: TMLHE | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for TMLHE(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: TMLHE |
Familial Cancer Database: TMLHE |
* 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/ |
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REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: TMLHE |
MedGen: TMLHE (Human Medical Genetics with Condition) | |
ClinVar: TMLHE | |
Phenotype | MGI: TMLHE (International Mouse Phenotyping Consortium) |
PhenomicDB: TMLHE |
Mutations for TMLHE |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TMLHE 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=32) | (# total SNVs=11) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr23:154754254-154754254 | p.V74A | 3 |
chr23:154754197-154754197 | p.R93H | 2 |
chr23:154736681-154736681 | p.L291L | 2 |
chr23:154743676-154743676 | p.E203E | 1 |
chr23:154736560-154736560 | p.R332W | 1 |
chr23:154743910-154743910 | p.V125V | 1 |
chr23:154736731-154736731 | p.F275I | 1 |
chr23:154754274-154754274 | p.T67T | 1 |
chr23:154743709-154743709 | p.V192V | 1 |
chr23:154736575-154736575 | p.E327* | 1 |
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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 |   | 6 |   |   | 2 |   | 1 |   |   | 5 | 2 |   |   |   | 2 | 5 |   | 6 |
# mutation | 1 | 1 |   | 5 |   |   | 2 |   | 2 |   |   | 5 | 2 |   |   |   | 2 | 5 |   | 7 |
nonsynonymous SNV |   |   |   | 4 |   |   | 2 |   | 1 |   |   | 4 | 1 |   |   |   | 2 | 3 |   | 3 |
synonymous SNV | 1 | 1 |   | 1 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   |   | 2 |   | 4 |
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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* 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 |
chrX:154754254 | p.V74A,TMLHE | 3 |
chrX:154736681 | p.L291L,TMLHE | 2 |
chrX:154741379 | p.Q283K,TMLHE | 1 |
chrX:154754204 | p.H91Y,TMLHE | 1 |
chrX:154736637 | p.F275L,TMLHE | 1 |
chrX:154741382 | p.T90T,TMLHE | 1 |
chrX:154754205 | p.C259F,TMLHE | 1 |
chrX:154736649 | p.E250E,TMLHE | 1 |
chrX:154741390 | p.T67I,TMLHE | 1 |
chrX:154736668 | p.R241R,TMLHE | 1 |
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* 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. |
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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 TMLHE |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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ATF7IP,CUL4B,FMR1,MTM1,MTMR1,NCKAP1,PHF6, RAB10,RBM41,RBMXL1,RLIM,SLC9A7,SOS1,SPRY3, STAG2,TMLHE,USP34,VAMP7,VBP1,VMA21,ZFYVE9 | ADHFE1,TCAIM,CLASP1,CS,ETFDH,EYA1,GKAP1, GNPAT,IARS2,IPO5,KIAA0368,L2HGDH,MUT,NIPSNAP3B, PPARA,PTCD2,RMND5A,SUCLA2,SUCLG2,TMLHE,UQCRC2 | ||||
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ABCB7,ARMCX5,BRCC3,C1GALT1C1,CXorf40B,CXorf56,ENOX2, LAMP2,MCTS1,NKAP,NSDHL,OCRL,PGRMC1,JADE3, PSMD10,RNF113A,STAG2,TIMM8A,TMLHE,VBP1,ZBTB33 | ABHD4,ALDH2,ATMIN,EGLN1,EPB41L5,H1F0,LRRC6, METTL7A,MPI,PDK3,PPAP2A,PPM1A,PPP1R3D,PTEN, PTENP1,RTN3,SLC16A1,STBD1,SUOX,TAB2,TMLHE |
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* 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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Pharmacological Information for TMLHE |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00126 | trimethyllysine hydroxylase, epsilon | approved; nutraceutical | Vitamin C | ![]() | ![]() |
DB00139 | trimethyllysine hydroxylase, epsilon | approved; nutraceutical | Succinic acid | ![]() | ![]() |
DB00145 | trimethyllysine hydroxylase, epsilon | approved; nutraceutical | Glycine | ![]() | ![]() |
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Cross referenced IDs for TMLHE |
* 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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