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mutLBSgeneDB |
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| Gene summary for RAB28 |
 Gene summary |
| Basic gene Info. | Gene symbol | RAB28 |
| Gene name | RAB28, member RAS oncogene family | |
| Synonyms | CORD18 | |
| Cytomap | UCSC genome browser: 4p15.33 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001017979.2, NM_001159601.1,NM_004249.3, | |
| Description | ras-related protein Rab-28 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 612994 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000157869 | ||
| HPRD : 06699 | ||
| Vega : OTTHUMG00000090543 | ||
| Protein | UniProt: P51157 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RAB28 | |
| BioGPS: 9364 | ||
| Pathway | NCI Pathway Interaction Database: RAB28 | |
| KEGG: RAB28 | ||
| REACTOME: RAB28 | ||
| Pathway Commons: RAB28 | ||
| Context | iHOP: RAB28 | |
| ligand binding site mutation search in PubMed: RAB28 | ||
| UCL Cancer Institute: RAB28 | ||
| 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 RAB28 |
| 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 | S159 | S159L | BRCA | 1 | N129 | N129S | LUAD | 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 RAB28 |
| 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 | S159 | S159L | 0.041177995 | N129 | N129S | -1.2939679 |
| (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 RAB28 from PDB |
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| Differential gene expression and gene-gene network for RAB28 |
| 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 RAB28 |
| 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 RAB28 |
| 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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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of RAB28 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | G3D | PPGP | 2hxs | A | N129 S159 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 3e5h | A | N129 S159 |
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| Conservation information for LBS of RAB28 |
| Multiple alignments for P51157 in multiple species |
| LBS | AA sequence | # species | Species | A160 | SHFVSAKTGDS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | A22 | VLGDGTSGKTS | 3 | Bos taurus, Mus musculus, Rattus norvegicus | A22 | VLGDGASGKTS | 1 | Homo sapiens | D132 | VGNKIDLEHMR | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F37 | FAQETFGKQYK | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G21 | VVLGDGTSGKT | 3 | Bos taurus, Mus musculus, Rattus norvegicus | G21 | VVLGDGASGKT | 1 | Homo sapiens | G24 | GDGTSGKTSLA | 3 | Bos taurus, Mus musculus, Rattus norvegicus | G24 | GDGASGKTSLT | 1 | Homo sapiens | G38 | AQETFGKQYKQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G71 | VWDIGGQTIGG | 3 | Bos taurus, Mus musculus, Rattus norvegicus | G71 | IWDIGGQTIGG | 1 | Homo sapiens | K130 | ALVGNKIDLEH | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K161 | HFVSAKTGDSV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K25 | DGTSGKTSLAT | 3 | Bos taurus, Mus musculus, Rattus norvegicus | K25 | DGASGKTSLTT | 1 | Homo sapiens | K39 | QETFGKQYKQT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L133 | GNKIDLEHMRT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | N129 | VALVGNKIDLE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Q43 | GKQYKQTIGLD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | S159 | SSHFVSAKTGD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | S23 | LGDGTSGKTSL | 3 | Bos taurus, Mus musculus, Rattus norvegicus | S23 | LGDGASGKTSL | 1 | Homo sapiens | S27 | TSGKTSLATCF | 3 | Bos taurus, Mus musculus, Rattus norvegicus | S27 | ASGKTSLTTCF | 1 | Homo sapiens | T26 | GTSGKTSLATC | 3 | Bos taurus, Mus musculus, Rattus norvegicus | T26 | GASGKTSLTTC | 1 | Homo sapiens | T44 | KQYKQTIGLDF | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y41 | TFGKQYKQTIG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus |
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