mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 RNASE4
Gene summary
Basic gene Info.Gene symbolRNASE4
Gene nameribonuclease, RNase A family, 4
SynonymsRAB1|RNS4
CytomapUCSC genome browser: 14q11
Type of geneprotein-coding
RefGenesNM_001282192.1,
NM_001282193.1,NM_002937.4,NM_194431.2,NM_194430.1,
DescriptionRNase 4ribonuclease 4ribonuclease A B1
Modification date20141207
dbXrefs MIM : 601030
HGNC : HGNC
Ensembl : ENSG00000258818
HPRD : 03018
Vega : OTTHUMG00000029575
ProteinUniProt: P34096
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RNASE4
BioGPS: 6038
PathwayNCI Pathway Interaction Database: RNASE4
KEGG: RNASE4
REACTOME: RNASE4
Pathway Commons: RNASE4
ContextiHOP: RNASE4
ligand binding site mutation search in PubMed: RNASE4
UCL Cancer Institute: RNASE4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


Top
Ligand binding site mutations for RNASE4

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R129R129TBLCA1
R129V131ICOAD1
R129R130CGBM1
G19G19ELUAD1
F145G147DSKCM1
Q39R38QSTAD1
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.


Top
Protein structure related information for RNASE4
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.
LBSAAchange of nsSNVRelative stability change
R129R130C-1.0776191
R129R129T-1.0670892
F145G147D-0.92200932
Q39R38Q-0.82638079
G19G19E-0.63493091
R129V131I-0.62698526
(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 RNASE4 from PDB

Top
Differential gene expression and gene-gene network for RNASE4
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 RNASE4 and the right PPI network was created from samples without mutations in the LBS of RNASE4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Top

Top
Phenotype information for RNASE4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023893Liver Cirrhosis, Experimental1Biomarker
umls:C0033578Prostatic Neoplasms1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Top
Pharmacological information for RNASE4
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 statusDrugBank IDNameTypeDrug structure
ExperimentalDB034482'-Deoxyuridine 3'-MonophosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RNASE4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


Top
Conservation information for LBS of RNASE4
Multiple alignments for P34096 in multiple species
LBSAA sequence# speciesSpecies
D30PSYGQDGMYQR2Homo sapiens, Pan troglodytes
D30PSYGQDRMYQR1Rattus norvegicus
F145QVPVHFDG2Homo sapiens, Pan troglodytes
F145EVPVHFDR1Rattus norvegicus
F70YHCKRFNTFIH2Homo sapiens, Pan troglodytes
F70TQCKRFNTFIH1Rattus norvegicus
G19LLTLLGLGLVQ3Homo sapiens, Pan troglodytes, Rattus norvegicus
H144PQVPVHFDG2Homo sapiens, Pan troglodytes
H144PEVPVHFDR1Rattus norvegicus
H40RFLRQHVHPEE2Homo sapiens, Pan troglodytes
H40RFLRQHVDPEG1Rattus norvegicus
K68TLYHCKRFNTF2Homo sapiens, Pan troglodytes
K68TSTQCKRFNTF1Rattus norvegicus
N71HCKRFNTFIHE2Homo sapiens, Pan troglodytes
N71QCKRFNTFIHE1Rattus norvegicus
Q39QRFLRQHVHPE2Homo sapiens, Pan troglodytes
Q39QRFLRQHVDPE1Rattus norvegicus
R129AIASTRRVVIA1Homo sapiens
R129AMASTRRVVIA1Pan troglodytes
R129ARASTRRVVIA1Rattus norvegicus
R35DGMYQRFLRQH2Homo sapiens, Pan troglodytes
R35DRMYQRFLRQH1Rattus norvegicus
T72CKRFNTFIHED3Homo sapiens, Pan troglodytes, Rattus norvegicus


Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas