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 GZMA

Gene summary

Basic gene Info.	Gene symbol	GZMA
	Gene name	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)
	Synonyms	CTLA3\|HFSP
	Cytomap	UCSC genome browser: 5q11-q12
	Type of gene	protein-coding
	RefGenes	NM_006144.3,
	Description	CTL tryptaseGranzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)HFcytotoxic T-lymphocyte proteinase 1fragmentin-1granzyme Ah factor
	Modification date	20141207
dbXrefs	MIM : 140050
	HGNC : HGNC
	Ensembl : ENSG00000145649
	HPRD : 00771
	Vega : OTTHUMG00000097011
Protein	UniProt: P12544 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GZMA
	BioGPS: 3001
Pathway	NCI Pathway Interaction Database: GZMA
	KEGG: GZMA
	REACTOME: GZMA
	Pathway Commons: GZMA
Context	iHOP: GZMA
	ligand binding site mutation search in PubMed: GZMA
	UCL Cancer Institute: GZMA
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:0032078	negative regulation of endodeoxyribonuclease activity	12524539
GO:0043065	positive regulation of apoptotic process	12524539
GO:0043392	negative regulation of DNA binding	12524539
GO:0051354	negative regulation of oxidoreductase activity	12524539
GO:0051603	proteolysis involved in cellular protein catabolic process	12524539

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Ligand binding site mutations for GZMA

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
D206	G204E	BLCA	1
D206	R205K	BLCA	1
R111	R111C	HNSC	1
G241	G241C	LUAD	1
C234	G235R	PRAD	1
R111	E112K	SKCM	1
S212,G210	D211E	SKCM	1
S227	S227F	SKCM	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 GZMA

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
G210	D211E	-1.1087894
S212	D211E	-1.1087894
C234	G235R	-0.91335917
D206	G204E	-0.78827461
D206	R205K	-0.68623478
R111	R111C	-0.61211885
R111	E112K	-0.2822435
S227	S227F	-0.23679094
G241	G241C	-0.050079002

(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 GZMA from PDB

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Differential gene expression and gene-gene network for GZMA

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

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 GZMA

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.