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 APOBEC3G

Gene summary

Basic gene Info.	Gene symbol	APOBEC3G
	Gene name	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G
	Synonyms	A3G\|ARCD\|ARP-9\|ARP9\|CEM-15\|CEM15\|bK150C2.7\|dJ494G10.1
	Cytomap	UCSC genome browser: 22q13.1-q13.2
	Type of gene	protein-coding
	RefGenes	NM_021822.3,
	Description	APOBEC-related cytidine deaminaseAPOBEC-related protein 9DNA dC->dU editing enzymeDNA dC->dU-editing enzyme APOBEC-3Gapolipoprotein B editing enzyme catalytic polypeptide-like 3Gapolipoprotein B mRNA editing enzyme cytidine deaminaseapolipoprotein B
	Modification date	20141222
dbXrefs	MIM : 607113
	HGNC : HGNC
	Ensembl : ENSG00000239713
	HPRD : 06172
	Vega : OTTHUMG00000151081
Protein	UniProt: Q9HC16 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_APOBEC3G
	BioGPS: 60489
Pathway	NCI Pathway Interaction Database: APOBEC3G
	KEGG: APOBEC3G
	REACTOME: APOBEC3G
	Pathway Commons: APOBEC3G
Context	iHOP: APOBEC3G
	ligand binding site mutation search in PubMed: APOBEC3G
	UCL Cancer Institute: APOBEC3G
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:0002230	positive regulation of defense response to virus by host	17121840
GO:0009972	cytidine deamination	16378963
GO:0010529	negative regulation of transposition	16527742
GO:0045071	negative regulation of viral genome replication	16378963
GO:0045087	innate immune response	17121840
GO:0045869	negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	16571802
GO:0048525	negative regulation of viral process	17121840
GO:0051607	defense response to virus	12808465
GO:0070383	DNA cytosine deamination	16527742

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Ligand binding site mutations for APOBEC3G

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
G214	R215W	GBM	1
G214	R215P	OV	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 APOBEC3G

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
G214	R215P	-1.3941606
G214	R215W	-1.2854938

(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 APOBEC3G from PDB

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Differential gene expression and gene-gene network for APOBEC3G

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 APOBEC3G and the right PPI network was created from samples without mutations in the LBS of APOBEC3G. 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 APOBEC3G

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 APOBEC3G

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.