mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	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 RAB11A

Gene summary

Basic gene Info.	Gene symbol	RAB11A
	Gene name	RAB11A, member RAS oncogene family
	Synonyms	YL8
	Cytomap	UCSC genome browser: 15q22.31
	Type of gene	protein-coding
	RefGenes	NM_001206836.1, NM_004663.4,
	Description	RAB 11A, member oncogene familyrab-11ras-related protein Rab-11A
	Modification date	20141207
dbXrefs	MIM : 605570
	HGNC : HGNC
	Ensembl : ENSG00000103769
	HPRD : 05715
	Vega : OTTHUMG00000133162
Protein	UniProt: P62491 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAB11A
	BioGPS: 8766
Pathway	NCI Pathway Interaction Database: RAB11A
	KEGG: RAB11A
	REACTOME: RAB11A
	Pathway Commons: RAB11A
Context	iHOP: RAB11A
	ligand binding site mutation search in PubMed: RAB11A
	UCL Cancer Institute: RAB11A
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:0006184	GTP catabolic process	17562788
GO:0016192	vesicle-mediated transport	17462998
GO:0072659	protein localization to plasma membrane	17082457

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Ligand binding site mutations for RAB11A

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
R129	R129H	UCEC	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 RAB11A

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.

LBS	AAchange of nsSNV	Relative stability change
R129	R129H	-1.1418758

(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 RAB11A from PDB

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Differential gene expression and gene-gene network for RAB11A

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 RAB11A and the right PPI network was created from samples without mutations in the LBS of RAB11A. 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 RAB11A

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0263454	Chloracne	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RAB11A

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 status	DrugBank ID	Name	Type	Drug structure
Experimental	DB01864	5'-Guanosine-Diphosphate-Monothiophosphate	Small molecule
Experimental	DB04315	Guanosine-5'-Diphosphate	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RAB11A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
2ME		METHOXYETHANE	2hv8	B	R129

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Conservation information for LBS of RAB11A

Multiple alignments for P62491 in multiple species

LBS	AA sequence	# species	Species
A155	FIETSALDSTN	5	Homo sapiens, Gallus gallus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
A155	FTETSALNSEN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A155	FMETSALEALN	1	Arabidopsis thaliana
A155	FMETSALESMN	1	Arabidopsis thaliana
A155	FIETSALDYTN	1	Bos taurus
A155	FIETSAMDASN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A68	QIWDTAGQERY	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D127	VGNKSDLRHLR	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
D127	VGNKADLRHLR	2	Arabidopsis thaliana, Arabidopsis thaliana
D127	IGNKSDLAHLR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D127	VGNKTDLLHLR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E39	NEFNLESKSTI	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
E39	NEFSLESKSTI	2	Arabidopsis thaliana, Arabidopsis thaliana
E39	NEFNMDSKSTI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E39	NEFNIESKSTI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F36	FTRNEFNLESK	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
F36	FTRNEFSLESK	2	Arabidopsis thaliana, Arabidopsis thaliana
F36	FTKNEFNMDSK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F36	FTRNEFNIESK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G21	LIGDSGVGKSN	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G23	GDSGVGKSNLL	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G69	IWDTAGQERYR	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K125	MLVGNKSDLRH	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
K125	GLIGNKSDLAH	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K125	MLVGNKADLRH	1	Arabidopsis thaliana
K125	MFVGNKADLRH	1	Arabidopsis thaliana
K125	MLVGNKTDLLH	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K24	DSGVGKSNLLS	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
K24	DSGVGKSNLLM	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K41	FNLESKSTIGV	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
K41	FSLESKSTIGV	2	Arabidopsis thaliana, Arabidopsis thaliana
K41	FNMDSKSTIGV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K41	FNIESKSTIGV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L128	GNKSDLRHLRA	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
L128	GNKADLRHLRA	2	Arabidopsis thaliana, Arabidopsis thaliana
L128	GNKSDLAHLRA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L128	GNKTDLLHLRA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L156	IETSALDSTNV	5	Homo sapiens, Gallus gallus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
L156	TETSALNSENV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L156	METSALEALNV	1	Arabidopsis thaliana
L156	METSALESMNV	1	Arabidopsis thaliana
L156	IETSALDYTNV	1	Bos taurus
L156	IETSAMDASNV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L38	RNEFNLESKST	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
L38	RNEFSLESKST	2	Arabidopsis thaliana, Arabidopsis thaliana
L38	KNEFNMDSKST	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L38	RNEFNIESKST	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N124	IMLVGNKSDLR	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
N124	VGLIGNKSDLA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N124	IMLVGNKADLR	1	Arabidopsis thaliana
N124	IMFVGNKADLR	1	Arabidopsis thaliana
N124	IMLVGNKTDLL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N26	GVGKSNLLSRF	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
N26	GVGKSNLLMRF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N37	TRNEFNLESKS	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
N37	TRNEFSLESKS	2	Arabidopsis thaliana, Arabidopsis thaliana
N37	TKNEFNMDSKS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N37	TRNEFNIESKS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R129	NKSDLRHLRAV	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
R129	NKADLRHLRAV	2	Arabidopsis thaliana, Arabidopsis thaliana
R129	NKSDLAHLRAV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R129	NKTDLLHLRAV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R132	DLRHLRAVPTD	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
R132	DLRHLRAVSTE	2	Arabidopsis thaliana, Arabidopsis thaliana
R132	DLAHLRAVPTE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R132	DLLHLRAVSTE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S154	SFIETSALDST	5	Homo sapiens, Gallus gallus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
S154	LFTETSALNSE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S154	FFMETSALEAL	1	Arabidopsis thaliana
S154	FFMETSALESM	1	Arabidopsis thaliana
S154	SFIETSALDYT	1	Bos taurus
S154	SFIETSAMDAS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S20	VLIGDSGVGKS	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S25	SGVGKSNLLSR	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
S25	SGVGKSNLLMR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S40	EFNLESKSTIG	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
S40	EFSLESKSTIG	2	Arabidopsis thaliana, Arabidopsis thaliana
S40	EFNMDSKSTIG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S40	EFNIESKSTIG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S42	NLESKSTIGVE	6	Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
S42	SLESKSTIGVE	2	Arabidopsis thaliana, Arabidopsis thaliana
S42	NMDSKSTIGVE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S42	NIESKSTIGVE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T43	LESKSTIGVEF	8	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus
T43	MDSKSTIGVEF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T43	IESKSTIGVEF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V22	IGDSGVGKSNL	10	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843)