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 CTSF

Gene summary

Basic gene Info.	Gene symbol	CTSF
	Gene name	cathepsin F
	Synonyms	CATSF\|CLN13
	Cytomap	UCSC genome browser: 11q13
	Type of gene	protein-coding
	RefGenes	NM_003793.3,
	Description	-
	Modification date	20141219
dbXrefs	MIM : 603539
	HGNC : HGNC
	Ensembl : ENSG00000174080
	HPRD : 04643
	Vega : OTTHUMG00000167090
Protein	UniProt: Q9UBX1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CTSF
	BioGPS: 8722
Pathway	NCI Pathway Interaction Database: CTSF
	KEGG: CTSF
	REACTOME: CTSF
	Pathway Commons: CTSF
Context	iHOP: CTSF
	ligand binding site mutation search in PubMed: CTSF
	UCL Cancer Institute: CTSF
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

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Ligand binding site mutations for CTSF

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
W453	G454S	BRCA	1
L337	L337M	COAD	1
M334	C333F	LUAD	1
Q410	G408D	STAD	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 CTSF

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
M334	C333F	-1.3042529
W453	G454S	-0.98849702
Q410	G408D	-0.81702822
L337	L337M	-0.7516526

(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 CTSF from PDB

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Differential gene expression and gene-gene network for CTSF

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C3715049	CEROID LIPOFUSCINOSIS, NEURONAL, 13	1	GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for CTSF

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	DB01810	[1-(1-Methyl-4,5-Dioxo-Pent-2-Enylcarbamoyl)-2-Phenyl-Ethyl]-Carbamic Acid Benzyl Ester	Small molecule
Experimental	DB01871	[1-(1-Benzyl-3-Hydroxy-2-Oxo-Propylcarbamoyl)-2-Phenyl-Ethyl]-Carbamic Acid Benzyl Ester	Small molecule
Experimental	DB02243	4-Morpholin-4-Yl-Piperidine-1-Carboxylic Acid [1-(3-Benzenesulfonyl-1-Propyl-Allylcarbamoyl)-2-Phenylethyl]-Amide	Small molecule
Experimental	DB03536	Benzoyl-Arginine-Alanine-Methyl Ketone	Small molecule
Experimental	DB03573	WRR-99	Small molecule
Experimental	DB03691	WRR-112	Small molecule
Experimental	DB07913	HOMOPHENYLALANINYLMETHANE	Small molecule
Experimental	DB08775	BENZOYL-TYROSINE-ALANINE-METHYL KETONE	Small molecule