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 CP

Gene summary

Basic gene Info.	Gene symbol	CP
	Gene name	ceruloplasmin (ferroxidase)
	Synonyms	CP-2
	Cytomap	UCSC genome browser: 3q23-q25
	Type of gene	protein-coding
	RefGenes	NM_000096.3, NR_046371.1,
	Description	ceruloplasmin
	Modification date	20141219
dbXrefs	MIM : 117700
	HGNC : HGNC
	Ensembl : ENSG00000047457
	HPRD : 00317
	Vega : OTTHUMG00000159563
Protein	UniProt: P00450 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CP
	BioGPS: 1356
Pathway	NCI Pathway Interaction Database: CP
	KEGG: CP
	REACTOME: CP
	Pathway Commons: CP
Context	iHOP: CP
	ligand binding site mutation search in PubMed: CP
	UCL Cancer Institute: CP
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 CP

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
Y67	K68N	BRCA	1
H621	S622P	COAD	1
M709	G708D	GBM	1
T701	T701I	LUAD	1
D146	D146Y	LUSC	1
M259	Y260C	OV	1
G417	G418S	SKCM	1
K128	E129K	SKCM	1
K128	K128N	SKCM	1
M709	G708D	STAD	1
D703	D703G	UCEC	1
M709	G708S	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 CP

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
D146	D146Y	-1.4072974
M709	G708S	-1.2121492
M259	Y260C	-1.1685723
D703	D703G	-1.0815389
M709	G708D	-1.0081315
Y67	K68N	-0.98545644
H621	S622P	-0.82270847
K128	E129K	-0.78189387
G417	G418S	-0.61195306
K128	K128N	-0.5979672
T701	T701I	-0.10887518

(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 CP from PDB

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Differential gene expression and gene-gene network for CP

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0878682	Deficiency of ferroxidase	28	Biomarker, GeneticVariation
umls:C0019202	Hepatolenticular Degeneration	24	Biomarker
umls:C0282193	Iron Overload	12	Biomarker
umls:C0012715	Iron Metabolism Disorders	8	Biomarker
umls:C0011849	Diabetes Mellitus	6	Biomarker, GeneticVariation
umls:C0030567	Parkinson Disease	5	AlteredExpression, Biomarker, GeneticVariation
umls:C0018995	Hemochromatosis	5	Biomarker, GeneticVariation
umls:C0011854	Diabetes Mellitus, Type 1	3	Biomarker, GeneticVariation
umls:C0035304	Retinal Degeneration	3	Biomarker
umls:C0022116	Ischemia	3	Biomarker
umls:C0993582	Arthritis, Experimental	2	Biomarker
umls:C0004352	Autistic Disorder	2	Biomarker
umls:C2239176	Carcinoma, Hepatocellular	2	Biomarker
umls:C0017661	Glomerulonephritis, IGA	2	Biomarker
umls:C2931082	Familial apoceruloplasmin deficiency	2	Biomarker
umls:C0032914	Pre-Eclampsia	1	AlteredExpression, Biomarker
umls:C0001925	Albuminuria	1	Biomarker
umls:C0004134	Ataxia	1	Biomarker
umls:C0006111	Brain Diseases	1	Biomarker
umls:C0011156	Deficiency Diseases	1	Biomarker
umls:C0497327	Dementia	1	Biomarker
umls:C0013384	Dyskinesias	1	Biomarker
umls:C0027746	Nerve Degeneration	1	Therapeutic
umls:C0085397	Pasteurellaceae Infections	1	Biomarker
umls:C0033860	Psoriasis	1	Biomarker
umls:C0036341	Schizophrenia	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for CP

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.