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 SKP2

Gene summary

Basic gene Info.	Gene symbol	SKP2
	Gene name	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase
	Synonyms	FBL1\|FBXL1\|FLB1\|p45
	Cytomap	UCSC genome browser: 5p13
	Type of gene	protein-coding
	RefGenes	NM_001243120.1, NM_005983.3,NM_032637.3,
	Description	CDK2/cyclin A-associated protein p45F-box/LRR-repeat protein 1S-phase kinase-associated protein 2S-phase kinase-associated protein 2 (p45)p45skp2
	Modification date	20141207
dbXrefs	MIM : 601436
	HGNC : HGNC
	Ensembl : ENSG00000145604
	HPRD : 03256
	Vega : OTTHUMG00000131106
Protein	UniProt: Q13309 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SKP2
	BioGPS: 6502
Pathway	NCI Pathway Interaction Database: SKP2
	KEGG: SKP2
	REACTOME: SKP2
	Pathway Commons: SKP2
Context	iHOP: SKP2
	ligand binding site mutation search in PubMed: SKP2
	UCL Cancer Institute: SKP2
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 SKP2

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
D347	D347H	BRCA	1
H199	G200D	LUSC	1
H199	G200C	LUSC	1
H199	G200D	STAD	1
E214	S212I	STAD	1
T225	T225I	UCEC	1
G215	R217Q	UCEC	1
R294	G292S	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 SKP2

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
R294	G292S	-0.92494675
G215	R217Q	-0.80849539
E214	S212I	-0.65995733
D347	D347H	-0.55841005
H199	G200D	-0.29937886
H199	G200C	-0.16637812
T225	T225I	-0.14078365

(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 SKP2 from PDB

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Differential gene expression and gene-gene network for SKP2

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 SKP2 and the right PPI network was created from samples without mutations in the LBS of SKP2. 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 SKP2

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C2239176	Carcinoma, Hepatocellular	13	AlteredExpression, Biomarker
umls:C0027651	Neoplasms	3	AlteredExpression, Biomarker
umls:C0919267	Ovarian Neoplasms	3	AlteredExpression, Biomarker
umls:C0079744	Lymphoma, Large B-Cell, Diffuse	2	Biomarker
umls:C0025149	Medulloblastoma	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for SKP2

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.