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 UPP1

Gene summary

Basic gene Info.	Gene symbol	UPP1
	Gene name	uridine phosphorylase 1
	Synonyms	UDRPASE\|UP\|UPASE\|UPP
	Cytomap	UCSC genome browser: 7p12.3
	Type of gene	protein-coding
	RefGenes	NM_181597.1, NM_001287426.1,NM_001287428.1,NM_001287429.1,NM_001287430.1, NM_003364.3,NR_109837.1,
	Description	UPase 1urdPase 1
	Modification date	20141207
dbXrefs	MIM : 191730
	HGNC : HGNC
	Ensembl : ENSG00000183696
	HPRD : 08932
	Vega : OTTHUMG00000129253
Protein	UniProt: Q16831 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UPP1
	BioGPS: 7378
Pathway	NCI Pathway Interaction Database: UPP1
	KEGG: UPP1
	REACTOME: UPP1
	Pathway Commons: UPP1
Context	iHOP: UPP1
	ligand binding site mutation search in PubMed: UPP1
	UCL Cancer Institute: UPP1
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

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Ligand binding site mutations for UPP1

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
L273	R275C	BRCA	1
M110	I112L	COAD	1
H36	F37L	GBM	1
M110	M110I	LUAD	1
G143	G144R	LUAD	1
I247	R245L	LUSC	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 UPP1

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
I247	R245L	0.37450634
M110	I112L	-1.0877647
L273	R275C	-0.93788274
G143	G144R	-0.7056477
M110	M110I	-0.65610498
H36	F37L	-0.24151097

(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 UPP1 from PDB

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Differential gene expression and gene-gene network for UPP1

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 UPP1 and the right PPI network was created from samples without mutations in the LBS of UPP1. 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 UPP1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0162820	Dermatitis, Allergic Contact	1	Biomarker
umls:C0035228	Respiratory Hypersensitivity	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for UPP1

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
Investigational	DB05041	RP101	Small molecule
Experimental	DB07437	1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of UPP1 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
URF		5-FLUOROURACIL	3nbq	A	G143 I247 L273
URF		5-FLUOROURACIL	3nbq	B	G143 I247 L273
URF		5-FLUOROURACIL	3nbq	C	G143 I247 L273
URF		5-FLUOROURACIL	3nbq	D	G143 I247 L273
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	A	H36
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	B	H36
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	C	H36
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	D	H36
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	A	M110 G143 I247 L273
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	B	M110 G143 I247 L273
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	C	M110 G143 I247 L273
BAU		1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE	3euf	D	M110 G143 I247 L273

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Conservation information for LBS of UPP1

Multiple alignments for Q16831 in multiple species

LBS

AA sequence

# species

Species