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 ATAD2

Gene summary

Basic gene Info.	Gene symbol	ATAD2
	Gene name	ATPase family, AAA domain containing 2
	Synonyms	ANCCA\|CT137\|PRO2000
	Cytomap	UCSC genome browser: 8q24.13
	Type of gene	protein-coding
	RefGenes	NM_014109.3,
	Description	AAA nuclear coregulator cancer-associated proteinATPase family AAA domain-containing protein 2
	Modification date	20141207
dbXrefs	MIM : 611941
	HGNC : HGNC
	Ensembl : ENSG00000156802
	HPRD : 10678
	Vega : OTTHUMG00000165090
Protein	UniProt: Q6PL18 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ATAD2
	BioGPS: 29028
Pathway	NCI Pathway Interaction Database: ATAD2
	KEGG: ATAD2
	REACTOME: ATAD2
	Pathway Commons: ATAD2
Context	iHOP: ATAD2
	ligand binding site mutation search in PubMed: ATAD2
	UCL Cancer Institute: ATAD2
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0006200	ATP catabolic process	17998543
GO:0045893	positive regulation of transcription, DNA-templated	17998543

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Ligand binding site mutations for ATAD2

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
T1084,A1080	R1082T	BRCA	1
D1014	D1014N	COAD	1
D1020	D1020H	HNSC	1
E1017	E1017K	HNSC	1
R1005	D1003H	LUSC	1
I1056	D1054H	OV	1
D1014	D1014H	OV	1
D1014	P1015R	SKCM	1
D1071	R1072L	STAD	1
F992	F992L	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 ATAD2

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
E1017	E1017K	-1.3733934
D1020	D1020H	-1.1382667
A1080	R1082T	-1.0689562
T1084	R1082T	-1.0689562
I1056	D1054H	-1.0505786
F992	F992L	-1.0175282
D1014	P1015R	-0.99817843
R1005	D1003H	-0.75477621
D1014	D1014H	-0.74931551
D1014	D1014N	-0.74596632
D1071	R1072L	-0.37894701

(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 ATAD2 from PDB

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Differential gene expression and gene-gene network for ATAD2

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 ATAD2 and the right PPI network was created from samples without mutations in the LBS of ATAD2. 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 ATAD2

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0017661	Glomerulonephritis, IGA	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for ATAD2

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 ATAD2 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
38T		5-METHYLURIDINE	4qsw	A	D1014 E1017
37N		3-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-5-[(PHENYLSULFONYL) AMINO]BENZOIC ACID	4tu4	A	D1014 E1017
NP8		5-(5-METHOXYPYRIDIN-3-YL)-3-METHYL-8- [(PIPERIDIN-4-YL)AMINO]-1,2-DIHYDRO-1,7-NAPHTHYRIDIN- 2-ONE	5a5r	A	D1014 E1017 D1071
YD3		8-[[(3R,4R)-3-[[1,1-BIS(OXIDANYLIDENE)THIAN- 4-YL]METHOXY]PIPERIDIN-4-YL]AMINO]-3-METHYL-5- (5-METHYLPYRIDIN-3-YL)-1H-QUINOLIN-2-ONE	5a83	A	D1014 E1017 D1071
III		Peptide ligand (ARG,GLY,LYS,GLY,GLY)	4quu	A	D1020 D1071
III		Peptide ligand (SER,GLY,ARG,GLY,ALY,GLY)	4tt2	A	D1020 D1071
III		Peptide ligand (GLY,LEU,GLY,LYS,GLY)	4qut	A	D1071
JTF		8-{[2-(DIMETHYLAMINO)ETHYL]AMINO}-3-METHYL-1, 2-DIHYDROQUINOLIN-2-ONE	5a5p	A	D1071
78J		(3R,4R)-3-(CYCLOHEXYLMETHOXY)PIPERIDIN-4-YL] AMINO}-3-METHYL-1,2-DIHYDRO-1,7-NAPHTHYRIDIN- 2-ONE	5a81	A	D1071
THM		THYMIDINE	4qsv	A	E1017
6XC		3-METHYL-8-[(PIPERIDIN-4-YL)AMINO]-1,2- DIHYDRO-1,7-NAPHTHYRIDIN-2-ONE	5a5q	A	E1017 D1071
YEJ		8-[[(3R,4R)-3-[[1,1-BIS(OXIDANYLIDENE)THIAN- 4-YL]METHOXY]PIPERIDIN-4-YL]AMINO]-3-METHYL- 1H-1,7-NAPHTHYRIDIN-2-ONE	5a82	A	E1017 D1071
MPD		2-METHYLPENTANE-2,4-DIOL	4qss	A	F992
39R		3-(5-PHENYL-4H-1,2,4-TRIAZOL-3-YL)ANILINE	4tz2	A	I1056
ALY		N(6)-ACETYL-L-LYSINE	4tt4	B	R1005 A1080 T1084
III		Peptide ligand (SER,THR,GLY,GLY)	4tt4	B	T1084

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Conservation information for LBS of ATAD2

Multiple alignments for Q6PL18 in multiple species

LBS

AA sequence

# species

Species