mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 THBS1
Gene summary
Basic gene Info.Gene symbolTHBS1
Gene namethrombospondin 1
SynonymsTHBS|THBS-1|TSP|TSP-1|TSP1
CytomapUCSC genome browser: 15q15
Type of geneprotein-coding
RefGenesNM_003246.2,
Descriptionthrombospondin-1thrombospondin-1p180
Modification date20141207
dbXrefs MIM : 188060
HGNC : HGNC
HPRD : 01765
ProteinUniProt: P07996
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_THBS1
BioGPS: 7057
PathwayNCI Pathway Interaction Database: THBS1
KEGG: THBS1
REACTOME: THBS1
Pathway Commons: THBS1
ContextiHOP: THBS1
ligand binding site mutation search in PubMed: THBS1
UCL Cancer Institute: THBS1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0001937negative regulation of endothelial cell proliferation16150726
GO:0001953negative regulation of cell-matrix adhesion16150726
GO:0002581negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II16882710
GO:0002605negative regulation of dendritic cell antigen processing and presentation16882710
GO:0007050cell cycle arrest17596205
GO:0009749response to glucose18096704
GO:0010595positive regulation of endothelial cell migration18555217
GO:0010596negative regulation of endothelial cell migration18555217
GO:0010748negative regulation of plasma membrane long-chain fatty acid transport17416590
GO:0010751negative regulation of nitric oxide mediated signal transduction16150726
GO:0010754negative regulation of cGMP-mediated signaling17416590
GO:0010757negative regulation of plasminogen activation6438154
GO:0010763positive regulation of fibroblast migration18555217
GO:0016477cell migration18555217
GO:0016525negative regulation of angiogenesis16150726
GO:0018149peptide cross-linking3997886
GO:0030194positive regulation of blood coagulation3997886
GO:0030335positive regulation of cell migration15700281
GO:0030511positive regulation of transforming growth factor beta receptor signaling pathway18555217
GO:0030823regulation of cGMP metabolic process16150726
GO:0032026response to magnesium ion6777381
GO:0032695negative regulation of interleukin-12 production16882710
GO:0040037negative regulation of fibroblast growth factor receptor signaling pathway17996481
GO:0042535positive regulation of tumor necrosis factor biosynthetic process18726995
GO:0043032positive regulation of macrophage activation18757424
GO:0043066negative regulation of apoptotic process18653767
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process18653767
GO:0043536positive regulation of blood vessel endothelial cell migration18555217
GO:0043537negative regulation of blood vessel endothelial cell migration18555217
GO:0043652engulfment of apoptotic cell16882710
GO:0045727positive regulation of translation15700281
GO:0050921positive regulation of chemotaxis18555217
GO:0051592response to calcium ion18757424
GO:0051897positive regulation of protein kinase B signaling18653767
GO:0051918negative regulation of fibrinolysis6438154
GO:1902043positive regulation of extrinsic apoptotic signaling pathway via death domain receptors18726995
GO:2000353positive regulation of endothelial cell apoptotic process18726995
GO:2000379positive regulation of reactive oxygen species metabolic process18757424
GO:2001027negative regulation of endothelial cell chemotaxis16150726


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Ligand binding site mutations for THBS1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
P490I491NBRCA1
T507V506ACOAD1
G151G151SGBM1
Q209N207SHNSC1
T507V506LOV1
C451G452SSKCM1
R60E62KSKCM1
R47R46HSTAD1
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 THBS1
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
R60E62K-1.4875295
C451G452S-1.4737297
P490I491N-1.2484177
Q209N207S-1.2325661
R47R46H-0.97287759
T507V506A-0.88172492
G151G151S-0.20246358
T507V506L-0.19295518
(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 THBS1 from PDB

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Differential gene expression and gene-gene network for THBS1
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 THBS1 and the right PPI network was created from samples without mutations in the LBS of THBS1. 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 THBS1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1458155Breast Neoplasms4AlteredExpression, Biomarker, Therapeutic
umls:C0023890Liver Cirrhosis2Biomarker, GeneticVariation
umls:C0036341Schizophrenia2Biomarker
umls:C0011884Diabetic Retinopathy1Biomarker
umls:C0016059Fibrosis1Biomarker
umls:C0027707Nephritis, Interstitial1Biomarker
umls:C0035126Reperfusion Injury1Biomarker

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

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Pharmacological information for THBS1
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of THBS1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of THBS1
Multiple alignments for P07996 in multiple species
LBSAA sequence# speciesSpecies


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