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 SLIT2
Gene summary
Basic gene Info.Gene symbolSLIT2
Gene nameslit homolog 2 (Drosophila)
SynonymsSLIL3|Slit-2
CytomapUCSC genome browser: 4p15.2
Type of geneprotein-coding
RefGenesNM_001289135.1,
NM_001289136.1,NM_004787.2,
Descriptionslit homolog 2 protein
Modification date20141207
dbXrefs MIM : 603746
HGNC : HGNC
Ensembl : ENSG00000145147
HPRD : 04776
Vega : OTTHUMG00000128551
ProteinUniProt: O94813
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLIT2
BioGPS: 9353
PathwayNCI Pathway Interaction Database: SLIT2
KEGG: SLIT2
REACTOME: SLIT2
Pathway Commons: SLIT2
ContextiHOP: SLIT2
ligand binding site mutation search in PubMed: SLIT2
UCL Cancer Institute: SLIT2
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:0001933negative regulation of protein phosphorylation18345009
GO:0002689negative regulation of leukocyte chemotaxis11309622
GO:0007411axon guidance11748139
GO:0008045motor neuron axon guidance10102268
GO:0010593negative regulation of lamellipodium assembly16439689
GO:0010596negative regulation of endothelial cell migration18345009
GO:0014912negative regulation of smooth muscle cell migration16439689
GO:0021834chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration11748139
GO:0021836chemorepulsion involved in postnatal olfactory bulb interneuron migration15207848
GO:0030336negative regulation of cell migration19005219
GO:0030837negative regulation of actin filament polymerization19759280
GO:0031290retinal ganglion cell axon guidance10864954
GO:0043086negative regulation of catalytic activity16439689
GO:0043116negative regulation of vascular permeability18345009
GO:0048754branching morphogenesis of an epithelial tube18345009
GO:0048846axon extension involved in axon guidance16840550
GO:0050919negative chemotaxis11748139
GO:0050929induction of negative chemotaxis10197527
GO:0051058negative regulation of small GTPase mediated signal transduction16439689
GO:0071504cellular response to heparin17062560
GO:0071672negative regulation of smooth muscle cell chemotaxis16439689
GO:0071676negative regulation of mononuclear cell migration16439689
GO:0090024negative regulation of neutrophil chemotaxis19759280
GO:0090260negative regulation of retinal ganglion cell axon guidance17062560
GO:0090288negative regulation of cellular response to growth factor stimulus16439689


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Ligand binding site mutations for SLIT2
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
LBSAAchange of nsSNVCancer type# samples
H833S831YLUAD1
H833L832VOV1
H833G834RSKCM1
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 SLIT2
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
H833L832V-1.5278007
H833S831Y-0.49976779
H833G834R-0.47312092
(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 SLIT2 from PDB

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Differential gene expression and gene-gene network for SLIT2
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 SLIT2 and the right PPI network was created from samples without mutations in the LBS of SLIT2. 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 SLIT2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C2239176Carcinoma, Hepatocellular1Biomarker, PostTranslationalModification
umls:C0014556Epilepsy, Temporal Lobe1Biomarker
umls:C0149925Small Cell Lung Carcinoma1Biomarker

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

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Pharmacological information for SLIT2
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 SLIT2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SO4SULFATE2wfhAH833
SO4SULFATE2wfhBH833


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Conservation information for LBS of SLIT2
Multiple alignments for O94813 in multiple species
LBSAA sequence# speciesSpecies
A858HLAIGANPLYC2Homo sapiens, Mus musculus
A858HIAVGSNSLYC1Caenorhabditis elegans
H833RLLSLHGNDIS2Homo sapiens, Mus musculus
H833RILSLHGNDIS1Caenorhabditis elegans
Y810TLILSYNRLRC2Homo sapiens, Mus musculus
Y810TLIISYNKLRC1Caenorhabditis elegans


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