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mutLBSgeneDB |
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| Gene summary for ARF4 |
 Gene summary |
| Basic gene Info. | Gene symbol | ARF4 |
| Gene name | ADP-ribosylation factor 4 | |
| Synonyms | ARF2 | |
| Cytomap | UCSC genome browser: 3p14.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001660.3, | |
| Description | ADP-ribosylation factor 2 | |
| Modification date | 20141217 | |
| dbXrefs | MIM : 601177 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000168374 | ||
| HPRD : 03107 | ||
| Vega : OTTHUMG00000158601 | ||
| Protein | UniProt: P18085 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_ARF4 | |
| BioGPS: 378 | ||
| Pathway | NCI Pathway Interaction Database: ARF4 | |
| KEGG: ARF4 | ||
| REACTOME: ARF4 | ||
| Pathway Commons: ARF4 | ||
| Context | iHOP: ARF4 | |
| ligand binding site mutation search in PubMed: ARF4 | ||
| UCL Cancer Institute: ARF4 | ||
| 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:0006471 | protein ADP-ribosylation | 1899243 | GO:0016477 | cell migration | 22004728 | GO:0031584 | activation of phospholipase D activity | 12446727 | GO:0043066 | negative regulation of apoptotic process | 19041174 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 12446727 | GO:2000377 | regulation of reactive oxygen species metabolic process | 19041174 |
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| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | A27 | L25F | LUAD | 1 | E54 | N52D | SKCM | 1 | A27 | D26N | 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 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 |
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| 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 | A27 | L25F | -1.0737421 | E54 | N52D | -0.47758409 | A27 | D26N | -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 |
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| 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) |
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| Phenotype information for ARF4 |
| 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 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB04315 | Guanosine-5'-Diphosphate | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of ARF4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | GDP | GUANOSINE-5'-DIPHOSPHATE | 1z6x | A | A27 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1z6x | B | A27 | MG | MAGNESIUM(2+) | 1z6x | A | E54 | MG | MAGNESIUM(2+) | 1z6x | B | E54 |
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| Conservation information for LBS of ARF4 |
| Multiple alignments for P18085 in multiple species |
| LBS | AA sequence | # species | Species | A160 | VQATCATQGTG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A160 | IQSTCATQGHG | 1 | Drosophila melanogaster | A27 | MVGLDAAGKTT | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | A28 | VGLDAAGKTTI | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | C159 | YVQATCATQGT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C159 | FIQSTCATQGH | 1 | Drosophila melanogaster | D129 | FANKQDLPNAM | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | E54 | IGFNVETVEYK | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | G29 | GLDAAGKTTIL | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | K127 | LLFANKQDLPN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K127 | LVFANKQDLPN | 1 | Drosophila melanogaster | K30 | LDAAGKTTILY | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | L130 | ANKQDLPNAMA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L130 | ANKQDLPNAMT | 1 | Drosophila melanogaster | N126 | LLLFANKQDLP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N126 | LLVFANKQDLP | 1 | Drosophila melanogaster | T161 | QATCATQGTGL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T161 | QSTCATQGHGL | 1 | Drosophila melanogaster | T31 | DAAGKTTILYK | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus | T32 | AAGKTTILYKL | 4 | Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus |
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