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 PRKCQ

Gene summary

Basic gene Info.	Gene symbol	PRKCQ
	Gene name	protein kinase C, theta
	Synonyms	PRKCT\|nPKC-theta
	Cytomap	UCSC genome browser: 10p15
	Type of gene	protein-coding
	RefGenes	NM_001242413.2, NM_001282644.1,NM_001282645.1,NM_006257.4,
	Description	protein kinase C theta type
	Modification date	20141207
dbXrefs	MIM : 600448
	HGNC : HGNC
	Ensembl : ENSG00000065675
	HPRD : 02710
	Vega : OTTHUMG00000017623
Protein	UniProt: Q04759 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKCQ
	BioGPS: 5588
Pathway	NCI Pathway Interaction Database: PRKCQ
	KEGG: PRKCQ
	REACTOME: PRKCQ
	Pathway Commons: PRKCQ
Context	iHOP: PRKCQ
	ligand binding site mutation search in PubMed: PRKCQ
	UCL Cancer Institute: PRKCQ
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:0051092	positive regulation of NF-kappaB transcription factor activity	16356855

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Ligand binding site mutations for PRKCQ

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
A407	F406L	COAD	2
H270	H270N	BRCA	1
H232	R233S	BRCA	1
T442	T442M	BRCA	1
F668	F668L	COAD	1
A407	F406S	COAD	1
C173	C173F	HNSC	1
G464	G463R	LUAD	1
C245	E246K	LUSC	1
F664	N663S	OV	1
C262	D263N	SKCM	1
H160	E161K	SKCM	1
T442	T442M	STAD	1
C190	R191Q	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 PRKCQ

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
G464	G463R	0.024645446
C245	E246K	-1.3183809
H232	R233S	-1.2037417
C190	R191Q	-0.98538551
F668	F668L	-0.97975807
C262	D263N	-0.96990359
C173	C173F	-0.86467636
H270	H270N	-0.75068524
A407	F406S	-0.74546758
H160	E161K	-0.6966898
T442	T442M	-0.54019502
F664	N663S	-0.17861758
A407	F406L	-0.14758283

(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 PRKCQ from PDB

PDB ID	PDB title	PDB structure
1XJD	Crystal Structure of PKC-theta complexed with Staurosporine at 2A resolution

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Differential gene expression and gene-gene network for PRKCQ

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0003873	Arthritis, Rheumatoid	13	Biomarker, GeneticVariation
umls:C0011854	Diabetes Mellitus, Type 1	3	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for PRKCQ

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	DB02010	Staurosporine	Small molecule
Experimental	DB02482	Phosphonothreonine	Small molecule
Experimental	DB04522	Phosphonoserine	Small molecule

Gene-centered ligand-gene interaction network

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

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
PZW		(1R)-9-(AZETIDIN-3-YLAMINO)-1,8-DIMETHYL-3,5-DIHYDRO[1, 2,4]TRIAZINO[3,4-C][1,4]BENZOXAZIN-2(1H)-ONE	4q9z	B	A407
PZW		(1R)-9-(AZETIDIN-3-YLAMINO)-1,8-DIMETHYL-3,5-DIHYDRO[1, 2,4]TRIAZINO[3,4-C][1,4]BENZOXAZIN-2(1H)-ONE	4q9z	A	A407 F664
STU		STAUROSPORINE	1xjd	A	A407 G464
LG8		3-(8-DIMETHYLAMINOMETHYL-6,7,8,9-TETRAHYDRO-PYRIDO[1,2-A]INDOL-10-YL)-4-(1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE	2jed	B	A407 T442
3L0	(6-[(1,3-DIMETHYL-AZETIDIN-3-YL)-METHYL-AMINO]-4(R)- METHYL-7-PHENYL-2,10-DIHYDRO-9-OXA-1,2,4A-TRIAZA- PHENANTHREN-3-ONE)	(1R)-9-[(1,3-DIMETHYLAZETIDIN-3-YL)(METHYL)AMINO]-1- METHYL-8-PHENYL-3,5-DIHYDRO[1,2,4]TRIAZINO[3,4-C][1, 4]BENZOXAZIN-2(1H)-ONE	4ra5	B	A407 T442
LG8		3-(8-DIMETHYLAMINOMETHYL-6,7,8,9-TETRAHYDRO-PYRIDO[1,2-A]INDOL-10-YL)-4-(1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE	2jed	A	A407 T442 F664
3L0	(6-[(1,3-DIMETHYL-AZETIDIN-3-YL)-METHYL-AMINO]-4(R)- METHYL-7-PHENYL-2,10-DIHYDRO-9-OXA-1,2,4A-TRIAZA- PHENANTHREN-3-ONE)	(1R)-9-[(1,3-DIMETHYLAZETIDIN-3-YL)(METHYL)AMINO]-1- METHYL-8-PHENYL-3,5-DIHYDRO[1,2,4]TRIAZINO[3,4-C][1, 4]BENZOXAZIN-2(1H)-ONE	4ra5	A	A407 T442 F664 F668
ZN		ZINC(2+)	2enn	A	C173
ZN		ZINC(2+)	2enz	A	C245 H270
ZN		ZINC(2+)	2enn	A	H160 C190
ZN		ZINC(2+)	2enz	A	H232 C262

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Conservation information for LBS of PRKCQ

Multiple alignments for Q04759 in multiple species

LBS

AA sequence

# species

Species