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 RNASEL

Gene summary

Basic gene Info.	Gene symbol	RNASEL
	Gene name	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)
	Synonyms	PRCA1\|RNS4
	Cytomap	UCSC genome browser: 1q25
	Type of gene	protein-coding
	RefGenes	NM_021133.3,
	Description	2',5'-oligoisoadenylate synthetase-dependent2-5A-dependent RNase2-5A-dependent ribonucleaseRNase Linterferon-induced 2-5A-dependent RNaseribonuclease 4
	Modification date	20141207
dbXrefs	MIM : 180435
	HGNC : HGNC
	Ensembl : ENSG00000135828
	HPRD : 01590
	Vega : OTTHUMG00000035213
Protein	UniProt: Q05823 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RNASEL
	BioGPS: 6041
Pathway	NCI Pathway Interaction Database: RNASEL
	KEGG: RNASEL
	REACTOME: RNASEL
	Pathway Commons: RNASEL
Context	iHOP: RNASEL
	ligand binding site mutation search in PubMed: RNASEL
	UCL Cancer Institute: RNASEL
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:0045071	negative regulation of viral genome replication	19923450
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	19245366
GO:0051607	defense response to virus	19923450

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Ligand binding site mutations for RNASEL

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
I101	A102V	COAD	1
G58,W60	G59D	COAD	1
F647	K646T	COAD	1
G167	G168W	LUAD	1
I101	A102V	LUAD	1
Q34	V33A	SKCM	1
E55	F53L	UCEC	1
M644	K642E	UCEC	1
D505	S507N	UCEC	1
D485	D485Y	UCEC	1
I101	A99T	UCEC	1
R155	R155Q	UCEC	1
R310	R310W	UCEC	1
R400	R400H	UCEC	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 RNASEL

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
I101	A102V	0.35825025
R155	R155Q	-1.4767862
Q34	V33A	-1.3315772
D505	S507N	-1.2248697
W60	G59D	-1.0358632
G58	G59D	-1.0358632
R400	R400H	-1.0141247
M644	K642E	-0.76715948
D485	D485Y	-0.76084175
I101	A99T	-0.6716086
F647	K646T	-0.66119415
R310	R310W	-0.61865047
G167	G168W	-0.31624728
E55	F53L	-0.25806037

(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 RNASEL from PDB

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Differential gene expression and gene-gene network for RNASEL

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0033578	Prostatic Neoplasms	21	AlteredExpression, Biomarker, GeneticVariation
umls:C2931456	Prostate cancer, familial	15	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RNASEL

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.

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

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

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
MG		MAGNESIUM(2+)	4oau	C	D485 D505
MG		MAGNESIUM(2+)	4oav	B	D485 D505
ADP		ADP	4oau	C	D505
MG		MAGNESIUM(2+)	4oav	D	D505
25A		5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE	4g8l	B	E55 G58 W60 I101 R155
25A		5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE	4g8l	C	E55 G58 W60 I101 R155
NUC		Nucleic Acids	4oau	C	E55 G58 W60 I101 R155
NUC		Nucleic Acids	4oav	D	E55 G58 W60 I101 R155 G167
25A		5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE	1wdy	A	E55 G58 W60 R155
25A		5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE	4g8l	A	E55 G58 W60 R155
25A		5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE	4g8l	D	E55 G58 W60 R155
PUP		(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- YL)-4-HYDROXY-2-({[(S)-HYDROXY{[(2R,3S,4S)-4-HYDROXY- 2-(HYDROXYMETHYL)TETRAHYDROFURAN-3- YL]OXY}PHOSPHORYL]OXY}METHYL)TETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE	4oav	D	M644 F647
NUC		Nucleic Acids	4oav	B	Q34 E55 G58 W60 R155 G167
NUC		Nucleic Acids	4oav	B	R310
NUC		Nucleic Acids	4oav	D	R310
ACP		ADENOSINE 5'-[BETA,GAMMA-METHYLENE]TRIPHOSPHATE	4oav	B	R400 D505
ACP		ADENOSINE 5'-[BETA,GAMMA-METHYLENE]TRIPHOSPHATE	4oav	D	R400 D505

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Conservation information for LBS of RNASEL

Multiple alignments for Q05823 in multiple species

LBS

AA sequence

# species

Species