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 ARF4
Gene summary
Basic gene Info.Gene symbolARF4
Gene nameADP-ribosylation factor 4
SynonymsARF2
CytomapUCSC genome browser: 3p14.3
Type of geneprotein-coding
RefGenesNM_001660.3,
DescriptionADP-ribosylation factor 2
Modification date20141217
dbXrefs MIM : 601177
HGNC : HGNC
Ensembl : ENSG00000168374
HPRD : 03107
Vega : OTTHUMG00000158601
ProteinUniProt: P18085
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARF4
BioGPS: 378
PathwayNCI Pathway Interaction Database: ARF4
KEGG: ARF4
REACTOME: ARF4
Pathway Commons: ARF4
ContextiHOP: ARF4
ligand binding site mutation search in PubMed: ARF4
UCL Cancer Institute: ARF4
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
GO:0006471protein ADP-ribosylation1899243
GO:0016477cell migration22004728
GO:0031584activation of phospholipase D activity12446727
GO:0043066negative regulation of apoptotic process19041174
GO:0045944positive regulation of transcription from RNA polymerase II promoter12446727
GO:2000377regulation of reactive oxygen species metabolic process19041174


Top
Ligand binding site mutations for ARF4
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
A27L25FLUAD1
E54N52DSKCM1
A27D26NSKCM1
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 ARF4
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
A27L25F-1.0737421
E54N52D-0.47758409
A27D26N-0.3073369
(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 ARF4 from PDB

Top
Differential gene expression and gene-gene network for ARF4
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 ARF4 and the right PPI network was created from samples without mutations in the LBS of ARF4. 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 ARF4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Top
Pharmacological information for ARF4
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
ExperimentalDB04315Guanosine-5'-DiphosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of ARF4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
GDPGUANOSINE-5'-DIPHOSPHATE1z6xAA27
GDPGUANOSINE-5'-DIPHOSPHATE1z6xBA27
MGMAGNESIUM(2+)1z6xAE54
MGMAGNESIUM(2+)1z6xBE54


Top
Conservation information for LBS of ARF4
Multiple alignments for P18085 in multiple species
LBSAA sequence# speciesSpecies
A160VQATCATQGTG3Homo sapiens, Mus musculus, Rattus norvegicus
A160IQSTCATQGHG1Drosophila melanogaster
A27MVGLDAAGKTT4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
A28VGLDAAGKTTI4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
C159YVQATCATQGT3Homo sapiens, Mus musculus, Rattus norvegicus
C159FIQSTCATQGH1Drosophila melanogaster
D129FANKQDLPNAM4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
E54IGFNVETVEYK4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
G29GLDAAGKTTIL4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
K127LLFANKQDLPN3Homo sapiens, Mus musculus, Rattus norvegicus
K127LVFANKQDLPN1Drosophila melanogaster
K30LDAAGKTTILY4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
L130ANKQDLPNAMA3Homo sapiens, Mus musculus, Rattus norvegicus
L130ANKQDLPNAMT1Drosophila melanogaster
N126LLLFANKQDLP3Homo sapiens, Mus musculus, Rattus norvegicus
N126LLVFANKQDLP1Drosophila melanogaster
T161QATCATQGTGL3Homo sapiens, Mus musculus, Rattus norvegicus
T161QSTCATQGHGL1Drosophila melanogaster
T31DAAGKTTILYK4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus
T32AAGKTTILYKL4Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus


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