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 CDKL5
Gene summary
Basic gene Info.Gene symbolCDKL5
Gene namecyclin-dependent kinase-like 5
SynonymsEIEE2|ISSX|STK9
CytomapUCSC genome browser: Xp22
Type of geneprotein-coding
RefGenesNM_001037343.1,
NM_003159.2,
Descriptioncyclin dependent kinase 5 transcriptserine/threonine kinase 9serine/threonine-protein kinase 9
Modification date20141207
dbXrefs MIM : 300203
HGNC : HGNC
Ensembl : ENSG00000008086
HPRD : 02190
Vega : OTTHUMG00000021214
ProteinUniProt: O76039
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDKL5
BioGPS: 6792
PathwayNCI Pathway Interaction Database: CDKL5
KEGG: CDKL5
REACTOME: CDKL5
Pathway Commons: CDKL5
ContextiHOP: CDKL5
ligand binding site mutation search in PubMed: CDKL5
UCL Cancer Institute: CDKL5
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:0046777protein autophosphorylation16935860


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Ligand binding site mutations for CDKL5
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
E98E98KGBM1
V92,K94E93KLUAD1
C152L151QLUAD1
Y24V26GSTAD1
L142L141IUCEC1
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 CDKL5
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
C152L151Q-1.562275
V92E93K-1.1277787
K94E93K-1.1277787
Y24V26G-0.9955312
L142L141I-0.77077278
E98E98K-0.50194887
(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 CDKL5 from PDB

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Differential gene expression and gene-gene network for CDKL5
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 CDKL5 and the right PPI network was created from samples without mutations in the LBS of CDKL5. 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 CDKL5
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0035372Rett Syndrome59Biomarker, GeneticVariation
umls:C0036572Seizures35Biomarker, GeneticVariation
umls:C1839333Epileptic Encephalopathy, Early Infantile, 210Biomarker, GeneticVariation
umls:C0162635Angelman Syndrome2Biomarker

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

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Pharmacological information for CDKL5
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

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CDKL5 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
38R[4-({4-[(3-CYCLOPENTYL-1H-PYRAZOL-5-YL)AMINO] PYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE4bgqAY24 V92 K94 E98 L142 C152


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Conservation information for LBS of CDKL5
Multiple alignments for O76039 in multiple species
LBSAA sequence# speciesSpecies


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