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 L3MBTL1

Gene summary

Basic gene Info.	Gene symbol	L3MBTL1
	Gene name	l(3)mbt-like 1 (Drosophila)
	Synonyms	H-L(3)MBT\|L3MBTL\|ZC2HC3\|dJ138B7.3
	Cytomap	UCSC genome browser: 20q13.12
	Type of gene	protein-coding
	RefGenes	NM_015478.6, NM_032107.4,
	Description	l(3)mbt protein homologlethal (3) malignant brain tumor l(3)lethal(3)malignant brain tumor-like protein 1
	Modification date	20141207
dbXrefs	MIM : 608802
	HGNC : HGNC
	Ensembl : ENSG00000185513
	HPRD : 16387
	Vega : OTTHUMG00000032503
Protein	UniProt: Q9Y468 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_L3MBTL1
	BioGPS: 26013
Pathway	NCI Pathway Interaction Database: L3MBTL1
	KEGG: L3MBTL1
	REACTOME: L3MBTL1
	Pathway Commons: L3MBTL1
Context	iHOP: L3MBTL1
	ligand binding site mutation search in PubMed: L3MBTL1
	UCL Cancer Institute: L3MBTL1
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:0016568	chromatin modification	17540172
GO:0045652	regulation of megakaryocyte differentiation	18474616
GO:0045892	negative regulation of transcription, DNA-templated	17540172

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Ligand binding site mutations for L3MBTL1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
F379	D380H	BLCA	1
R461	R461M	COAD	1
D355	A353S	LUAD	1
Q250	P252L	LUAD	1
L361	L361F	SKCM	1
N358	M357I	SKCM	1
F379	F379V	STAD	1
D355	R356C	STAD	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 L3MBTL1

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
L361	L361F	-1.4555133
F379	D380H	-1.3466034
D355	A353S	-1.2710293
D355	R356C	-1.2380052
F379	F379V	-1.0883477
N358	M357I	-1.0025573
R461	R461M	-0.84632265
Q250	P252L	-0.051536499

(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 L3MBTL1 from PDB

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Differential gene expression and gene-gene network for L3MBTL1

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 L3MBTL1 and the right PPI network was created from samples without mutations in the LBS of L3MBTL1. 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 L3MBTL1

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 L3MBTL1

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.

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Experimental	DB03814	2-(N-Morpholino)-Ethanesulfonic Acid	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of L3MBTL1 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
LYS		LYSINE	3oq5	A	D355
MLY		N-DIMETHYL-LYSINE	2rhu	A	D355 F379
III		Peptide ligand (THR,LYS,LYS)	2rhi	A	D355 L361 F379
MLY		N-DIMETHYL-LYSINE	2rhx	A	D355 N358 F379
MLZ		N6-METHYL-L-LYSINE	2rhy	A	D355 N358 F379
III		Peptide ligand (ARG,HIS,ARG,LYS,VAL,LEU,ARG,ASP,ASN)	2pqw	A	D355 N358 L361
MES		2-(N-MORPHOLINIUMYL)ETHANESULFONATE	2rjc	A	D355 N358 L361 F379
MES		2-(N-MORPHOLINIUMYL)ETHANESULFONATE	2rjc	B	D355 N358 L361 F379
LYS		LYSINE	3oq5	C	D355 N358 L361 F379
P8H		3-BROMO-5-[(4-PYRROLIDIN-1-YLPIPERIDIN-1-YL)CARBONYL]PYRIDINE	3p8h	A	D355 N358 L361 F379
P8H		3-BROMO-5-[(4-PYRROLIDIN-1-YLPIPERIDIN-1-YL)CARBONYL]PYRIDINE	3p8h	B	D355 N358 L361 F379
UWN		[2-(PHENYLAMINO)BENZENE-1,4-DIYL]BIS{[4-(PYRROLIDIN-1-YL)PIPERIDIN-1-YL]METHANONE}	3uwn	A	D355 N358 L361 F379
MES		2-(N-MORPHOLINIUMYL)ETHANESULFONATE	2rjc	C	Q250
MES		2-(N-MORPHOLINIUMYL)ETHANESULFONATE	2rjc	A	R461
MES		2-(N-MORPHOLINIUMYL)ETHANESULFONATE	2rjc	C	R461

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Conservation information for LBS of L3MBTL1

Multiple alignments for Q9Y468 in multiple species

LBS

AA sequence

# species

Species