mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for TRMT61B

Gene summary

Basic gene Info.	Gene symbol	TRMT61B
	Gene name	tRNA methyltransferase 61B
	Synonyms	-
	Cytomap	UCSC genome browser: 2p23.2
	Type of gene	protein-coding
	RefGenes	NM_017910.3,
	Description	potential tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61Bpotential tRNA (adenine-N(1)-)-methyltransferase catalytic subunit TRMT61BtRNA (adenine(58)-N(1))-methyltransferase, mitochondrialtRNA methyltransferase 61 homolog B
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000171103
	HPRD : 07935
	Vega : OTTHUMG00000128433
Protein	UniProt: Q9BVS5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TRMT61B
	BioGPS: 55006
Pathway	NCI Pathway Interaction Database: TRMT61B
	KEGG: TRMT61B
	REACTOME: TRMT61B
	Pathway Commons: TRMT61B
Context	iHOP: TRMT61B
	ligand binding site mutation search in PubMed: TRMT61B
	UCL Cancer Institute: TRMT61B
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0051260	protein homooligomerization	23097428
GO:0070901	mitochondrial tRNA methylation	23097428

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Ligand binding site mutations for TRMT61B

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
T230	P232Q	LUAD	1
V279	V279L	SKCM	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, 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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Protein structure related information for TRMT61B

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
T230	P232Q	-1.4983137
V279	V279L	-1.0812155

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for TRMT61B from PDB

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Differential gene expression and gene-gene network for TRMT61B

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of TRMT61B and the right PPI network was created from samples without mutations in the LBS of TRMT61B. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

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Phenotype information for TRMT61B

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TRMT61B

Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.