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 CXCL12

Gene summary

Basic gene Info.	Gene symbol	CXCL12
	Gene name	chemokine (C-X-C motif) ligand 12
	Synonyms	IRH\|PBSF\|SCYB12\|SDF1\|TLSF\|TPAR1
	Cytomap	UCSC genome browser: 10q11.1
	Type of gene	protein-coding
	RefGenes	NM_000609.6, NM_001033886.2,NM_001178134.1,NM_001277990.1,NM_199168.3,
	Description	intercrine reduced in hepatomaspre-B cell growth-stimulating factorstromal cell-derived factor 1
	Modification date	20141222
dbXrefs	MIM : 600835
	HGNC : HGNC
	Ensembl : ENSG00000107562
	HPRD : 02904
	Vega : OTTHUMG00000018054
Protein	UniProt: P48061 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CXCL12
	BioGPS: 6387
Pathway	NCI Pathway Interaction Database: CXCL12
	KEGG: CXCL12
	REACTOME: CXCL12
	Pathway Commons: CXCL12
Context	iHOP: CXCL12
	ligand binding site mutation search in PubMed: CXCL12
	UCL Cancer Institute: CXCL12
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:0045785	positive regulation of cell adhesion	23620790
GO:0060326	cell chemotaxis	18308860
GO:0070098	chemokine-mediated signaling pathway	20388803
GO:0090026	positive regulation of monocyte chemotaxis	18802065
GO:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	20388803
GO:1903237	negative regulation of leukocyte tethering or rolling	18308860
GO:2000107	negative regulation of leukocyte apoptotic process	15059845
GO:2000406	positive regulation of T cell migration	23620790

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Ligand binding site mutations for CXCL12

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
P53	P53L	UCEC	1
E81,K85	L83P	UCEC	1
V70	C71Y	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 CXCL12

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
E81	L83P	-1.1193562
K85	L83P	-1.1193562
P53	P53L	-0.65745745
V70	C71Y	-0.28334952

(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 CXCL12 from PDB

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Differential gene expression and gene-gene network for CXCL12

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 CXCL12 and the right PPI network was created from samples without mutations in the LBS of CXCL12. 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 CXCL12

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0019693	HIV Infections	117	Biomarker, GeneticVariation
umls:C0027627	Neoplasm Metastasis	104	AlteredExpression, Biomarker
umls:C1458155	Breast Neoplasms	17	AlteredExpression, Biomarker, GeneticVariation
umls:C0033578	Prostatic Neoplasms	11	AlteredExpression, Biomarker, GeneticVariation
umls:C1956346	Coronary Artery Disease	11	Biomarker, GeneticVariation
umls:C2239176	Carcinoma, Hepatocellular	9	Biomarker, GeneticVariation
umls:C0022116	Ischemia	8	Biomarker
umls:C0027626	Neoplasm Invasiveness	2	Biomarker, GeneticVariation
umls:C0266929	Chronic Periodontitis	2	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for CXCL12

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.