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 symbolCXCL12
Gene namechemokine (C-X-C motif) ligand 12
CytomapUCSC genome browser: 10q11.1
Type of geneprotein-coding
Descriptionintercrine reduced in hepatomaspre-B cell growth-stimulating factorstromal cell-derived factor 1
Modification date20141222
dbXrefs MIM : 600835
Ensembl : ENSG00000107562
HPRD : 02904
Vega : OTTHUMG00000018054
ProteinUniProt: P48061
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CXCL12
BioGPS: 6387
PathwayNCI Pathway Interaction Database: CXCL12
Pathway Commons: CXCL12
ContextiHOP: CXCL12
ligand binding site mutation search in PubMed: CXCL12
UCL Cancer Institute: CXCL12
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0045785positive regulation of cell adhesion23620790
GO:0060326cell chemotaxis18308860
GO:0070098chemokine-mediated signaling pathway20388803
GO:0090026positive regulation of monocyte chemotaxis18802065
GO:1902230negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage20388803
GO:1903237negative regulation of leukocyte tethering or rolling18308860
GO:2000107negative regulation of leukocyte apoptotic process15059845
GO:2000406positive regulation of T cell migration23620790

Ligand binding site mutations for CXCL12

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

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.
LBSAAchange of nsSNVRelative stability change
(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

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.


Phenotype information for CXCL12
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0019693HIV Infections117Biomarker, GeneticVariation
umls:C0027627Neoplasm Metastasis104AlteredExpression, Biomarker
umls:C1458155Breast Neoplasms17AlteredExpression, Biomarker, GeneticVariation
umls:C0033578Prostatic Neoplasms11AlteredExpression, Biomarker, GeneticVariation
umls:C1956346Coronary Artery Disease11Biomarker, GeneticVariation
umls:C2239176Carcinoma, Hepatocellular9Biomarker, GeneticVariation
umls:C0027626Neoplasm Invasiveness2Biomarker, GeneticVariation
umls:C0266929Chronic Periodontitis2Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ApprovedDB06822TinzaparinSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CXCL12 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of CXCL12
Multiple alignments for P48061 in multiple species
LBSAA sequence# speciesSpecies

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