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 RPS5

Gene summary

Basic gene Info.	Gene symbol	RPS5
	Gene name	ribosomal protein S5
	Synonyms	S5
	Cytomap	UCSC genome browser: 19q13.4
	Type of gene	protein-coding
	RefGenes	NM_001009.3,
	Description	40S ribosomal protein S5
	Modification date	20141207
dbXrefs	MIM : 603630
	HGNC : HGNC
	Ensembl : ENSG00000083845
	HPRD : 04695
	Vega : OTTHUMG00000183530
Protein	UniProt: P46782 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS5
	BioGPS: 6193
Pathway	NCI Pathway Interaction Database: RPS5
	KEGG: RPS5
	REACTOME: RPS5
	Pathway Commons: RPS5
Context	iHOP: RPS5
	ligand binding site mutation search in PubMed: RPS5
	UCL Cancer Institute: RPS5
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

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Ligand binding site mutations for RPS5

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
I128	T126A	BRCA	1
N186	Y188C	COAD	1
N186	S187F	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 RPS5

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
I128	T126A	-0.9378811
N186	S187F	-0.9214149
N186	Y188C	-0.54176878

(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 RPS5 from PDB

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Differential gene expression and gene-gene network for RPS5

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 RPS5 and the right PPI network was created from samples without mutations in the LBS of RPS5. 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 RPS5

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 RPS5

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 RPS5 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
NUC		Nucleic Acids	5flx	F	I128 N186
NUC		Nucleic Acids	5a2q	F	N186

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Conservation information for LBS of RPS5

Multiple alignments for P46782 in multiple species

LBS	AA sequence	# species	Species
A131	TRIGRAGTVRR	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
A131	TRIGSAGTVRR	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
A131	TRIGSAGVVRR	2	Arabidopsis thaliana, Arabidopsis thaliana
A131	TRVGGGGAARR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G132	RIGRAGTVRRQ	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
G132	RIGSAGTVRRQ	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G132	RIGSAGVVRRQ	2	Arabidopsis thaliana, Arabidopsis thaliana
G132	RVGGGGAARRQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I128	EDSTRIGRAGT	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
I128	EDSTRIGSAGT	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
I128	EDATRIGSAGV	2	Arabidopsis thaliana, Arabidopsis thaliana
I128	EDTTRVGGGGA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K182	LINAAKGSSNS	8	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
K182	IINAAKGSSNS	2	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K182	LINAAKGSSTS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K191	NSYAIKKKDEL	8	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Caenorhabditis elegans, Drosophila melanogaster,
K191	NSYAIKKKDEI	2	Arabidopsis thaliana, Arabidopsis thaliana
K191	TSYAIKKKDEL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N186	AKGSSNSYAIK	10	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana, Arabidopsis thaliana, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Caen
N186	AKGSSTSYAIK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R130	STRIGRAGTVR	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
R130	STRIGSAGTVR	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
R130	ATRIGSAGVVR	2	Arabidopsis thaliana, Arabidopsis thaliana
R130	TTRVGGGGAAR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R135	RAGTVRRQAVD	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
R135	SAGTVRRQAVD	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
R135	SAGVVRRQAVD	2	Arabidopsis thaliana, Arabidopsis thaliana
R135	GGGAARRQAVD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S184	NAAKGSSNSYA	10	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana, Arabidopsis thaliana, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Caen
S184	NAAKGSSTSYA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T133	IGRAGTVRRQA	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
T133	IGSAGTVRRQA	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T133	IGSAGVVRRQA	2	Arabidopsis thaliana, Arabidopsis thaliana
T133	VGGGGAARRQA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V134	GRAGTVRRQAV	5	Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Bos taurus, Mus musculus
V134	GSAGTVRRQAV	3	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
V134	GSAGVVRRQAV	2	Arabidopsis thaliana, Arabidopsis thaliana
V134	GGGGAARRQAV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)