mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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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 RRAS
Gene summary
Basic gene Info.Gene symbolRRAS
Gene namerelated RAS viral (r-ras) oncogene homolog
Synonyms-
CytomapUCSC genome browser: 19q13.33
Type of geneprotein-coding
RefGenesNM_006270.3,
DescriptionOncogene RRASp23ras-related protein R-Ras
Modification date20141222
dbXrefs MIM : 165090
HGNC : HGNC
Ensembl : ENSG00000126458
HPRD : 01299
Vega : OTTHUMG00000183247
ProteinUniProt: P10301
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RRAS
BioGPS: 6237
PathwayNCI Pathway Interaction Database: RRAS
KEGG: RRAS
REACTOME: RRAS
Pathway Commons: RRAS
ContextiHOP: RRAS
ligand binding site mutation search in PubMed: RRAS
UCL Cancer Institute: RRAS
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


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Ligand binding site mutations for RRAS
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
S56Y58CUCEC1
N142V140FUCEC1
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 RRAS
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
S56Y58C-1.4454552
N142V140F-0.75163973
(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 RRAS from PDB

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Differential gene expression and gene-gene network for RRAS
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 RRAS and the right PPI network was created from samples without mutations in the LBS of RRAS. 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 RRAS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0033578Prostatic Neoplasms1Biomarker

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

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Pharmacological information for RRAS
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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RRAS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
GDPGUANOSINE-5'-DIPHOSPHATE2fn4AS56 N142


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Conservation information for LBS of RRAS
Multiple alignments for P10301 in multiple species
LBSAA sequence# speciesSpecies
A173YFEASAKLRLN3Homo sapiens, Mus musculus, Rattus norvegicus
A44GVGKSALTIQF3Homo sapiens, Mus musculus, Rattus norvegicus
D145VGNKADLESQR1Homo sapiens
D145VGNKADLENQR1Mus musculus
D145VGNKADLETQR1Rattus norvegicus
G39VVGGGGVGKSA3Homo sapiens, Mus musculus, Rattus norvegicus
G41GGGGVGKSALT3Homo sapiens, Mus musculus, Rattus norvegicus
K143VLVGNKADLES1Homo sapiens
K143VLVGNKADLEN1Mus musculus
K143VLVGNKADLET1Rattus norvegicus
K174FEASAKLRLNV3Homo sapiens, Mus musculus, Rattus norvegicus
K42GGGVGKSALTI3Homo sapiens, Mus musculus, Rattus norvegicus
L146GNKADLESQRQ1Homo sapiens
L146GNKADLENQRQ1Mus musculus
L146GNKADLETQRQ1Rattus norvegicus
N142IVLVGNKADLE2Mus musculus, Rattus norvegicus
N142VVLVGNKADLE1Homo sapiens
S172TYFEASAKLRL2Mus musculus, Rattus norvegicus
S172AYFEASAKLRL1Homo sapiens
S43GGVGKSALTIQ3Homo sapiens, Mus musculus, Rattus norvegicus
S56QSYFVSDYDPT3Homo sapiens, Mus musculus, Rattus norvegicus
V40VGGGGVGKSAL3Homo sapiens, Mus musculus, Rattus norvegicus


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