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 GGA1

Gene summary

Basic gene Info.	Gene symbol	GGA1
	Gene name	golgi-associated, gamma adaptin ear containing, ARF binding protein 1
	Synonyms	-
	Cytomap	UCSC genome browser: 22q13.31
	Type of gene	protein-coding
	RefGenes	NM_001001560.2, NM_001172687.1,NM_001172688.1,NM_013365.4,NM_001001561.2,
	Description	ADP-ribosylation factor binding protein 1ADP-ribosylation factor-binding protein GGA1gamma-adaptin related protein 1gamma-adaptin-related protein 1golgi associated, gamma adaptin ear containing, ARF binding protein 1golgi-localized, gamma ear-contain
	Modification date	20141207
dbXrefs	MIM : 606004
	HGNC : HGNC
	Ensembl : ENSG00000100083
	HPRD : 12078
	Vega : OTTHUMG00000030985
Protein	UniProt: Q9UJY5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GGA1
	BioGPS: 26088
Pathway	NCI Pathway Interaction Database: GGA1
	KEGG: GGA1
	REACTOME: GGA1
	Pathway Commons: GGA1
Context	iHOP: GGA1
	ligand binding site mutation search in PubMed: GGA1
	UCL Cancer Institute: GGA1
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 GGA1

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

LBS	AAchange of nsSNV	Cancer type	# samples
K131	I132M	HNSC	1
R89	R89C	LAML	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 GGA1

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
R89	R89C	-0.72993807
K131	I132M	-0.54852478

(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 GGA1 from PDB

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Differential gene expression and gene-gene network for GGA1

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 GGA1 and the right PPI network was created from samples without mutations in the LBS of GGA1. 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 GGA1

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 GGA1

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 status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GGA1 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (ASP,GLU,ASP,LEU,LEU,HIS,ILE)	1jwg	A	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1py1	A	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1py1	B	R89 K131
III		Peptide ligand (ASP,ILE,SER,LEU,LEU,LYS)	1py1	C	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1py1	D	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1ujj	A	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1ujk	A	R89 K131
III		Peptide ligand (ASP,ASP,ILE,SER,LEU,LEU,LYS)	1ujk	B	R89 K131
III		Peptide ligand (GLY,PHE,SER,ASP,ASP,VAL,PRO,MET,VAL,ILE,ALA)	3g2s	A	R89 K131
III		Peptide ligand (GLY,PHE,SER,ASP,ASP,VAL,PRO,MET,VAL,ILE,ALA)	3g2s	B	R89 K131
III		Peptide ligand (SER,ASP,ASP,VAL,PRO,MET,VAL,ILE,ALA)	3g2t	A	R89 K131
III		Peptide ligand (SER,ASP,ASP,VAL,PRO,MET,VAL,ILE,ALA)	3g2t	B	R89 K131
III		Peptide ligand (SER,ASP,GLU,ASP,LEU,LEU,GLU)	3g2u	A	R89 K131
III		Peptide ligand (SER,ASP,GLU,ASP,LEU,LEU,GLU)	3g2u	B	R89 K131
III		Peptide ligand (ASP,ASP,SER,ASP,GLU,ASP,LEU,LEU,GLU)	3g2v	A	R89 K131
III		Peptide ligand (SER,ASP,GLU,ASP,LEU,LEU,GLU)	3g2v	B	R89 K131
III		Peptide ligand (LEU,LEU,ASP,ASP,GLU,LEU,MET,SER,LEU)	3g2w	A	R89 K131
III		Peptide ligand (LEU,LEU,ASP,ASP,GLU,LEU,MET,SER)	3g2w	B	R89 K131

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Conservation information for LBS of GGA1

Multiple alignments for Q9UJY5 in multiple species

LBS

AA sequence

# species

Species