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 CHD4
Gene summary
Basic gene Info.Gene symbolCHD4
Gene namechromodomain helicase DNA binding protein 4
SynonymsCHD-4|Mi-2b|Mi2-BETA
CytomapUCSC genome browser: 12p13
Type of geneprotein-coding
RefGenesNM_001273.3,
NM_001297553.1,
DescriptionATP-dependent helicase CHD4Mi-2 autoantigen 218 kDa proteinchromodomain-helicase-DNA-binding protein 4
Modification date20141207
dbXrefs MIM : 603277
HGNC : HGNC
Ensembl : ENSG00000111642
HPRD : 04472
Vega : OTTHUMG00000169164
ProteinUniProt: Q14839
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHD4
BioGPS: 1108
PathwayNCI Pathway Interaction Database: CHD4
KEGG: CHD4
REACTOME: CHD4
Pathway Commons: CHD4
ContextiHOP: CHD4
ligand binding site mutation search in PubMed: CHD4
UCL Cancer Institute: CHD4
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:0043044ATP-dependent chromatin remodeling16217013


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Ligand binding site mutations for CHD4
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
C385L384MCOAD1
C475N477DCOAD1
H472Y471CCOAD1
C475H474YSKCM1
L461L461RSTAD1
C452R453QSTAD1
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 CHD4
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
C385L384M-1.3355119
L461L461R-1.2248183
C452R453Q-1.218975
H472Y471C-0.7780897
C475N477D-0.51759747
C475H474Y-0.40379998
(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 CHD4 from PDB

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Differential gene expression and gene-gene network for CHD4
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 CHD4 and the right PPI network was created from samples without mutations in the LBS of CHD4. 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 CHD4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0014170Endometrial Neoplasms1Biomarker
umls:C0036341Schizophrenia1Biomarker

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

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Pharmacological information for CHD4
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 CHD4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of CHD4
Multiple alignments for Q14839 in multiple species
LBSAA sequence# speciesSpecies
C373DHQDYCEVCQQ2Homo sapiens, Mus musculus
C373ENNDYCEECKQ1Caenorhabditis elegans
C373NHQENCEVCNQ1Caenorhabditis elegans
C373DDDDFVPKKDR1Arabidopsis thaliana
C373KLDEYIREEQV1Arabidopsis thaliana
C376DYCEVCQQGGE2Homo sapiens, Mus musculus
C376DYCEECKQDGE1Caenorhabditis elegans
C376ENCEVCNQDGE1Caenorhabditis elegans
C376DFVPKKDRTF-1Arabidopsis thaliana
C376EYIREEQV---1Arabidopsis thaliana
C385GEIILCDTCPR2Homo sapiens, Mus musculus
C385GELLLCDTCPR1Caenorhabditis elegans
C385GELMLCDTCTR1Caenorhabditis elegans
C385F----------1Arabidopsis thaliana
C385-----------1Arabidopsis thaliana
C388ILCDTCPRAYH2Homo sapiens, Mus musculus
C388-----------2Arabidopsis thaliana, Arabidopsis thaliana
C388LLCDTCPRAYH1Caenorhabditis elegans
C388MLCDTCTRAYH1Caenorhabditis elegans
C396AYHMVCLDPDM2Homo sapiens, Mus musculus
C396-----------2Arabidopsis thaliana, Arabidopsis thaliana
C396AYHTVCIDENM1Caenorhabditis elegans
C396AYHVACIDENM1Caenorhabditis elegans
C411EGKWSCPHCEK2Homo sapiens, Mus musculus
C411-----------2Arabidopsis thaliana, Arabidopsis thaliana
C411EGDWSCAHCIE1Caenorhabditis elegans
C411EGDWSCPHCEE1Caenorhabditis elegans
C414WSCPHCEKEGI2Homo sapiens, Mus musculus
C414-----------2Arabidopsis thaliana, Arabidopsis thaliana
C414WSCAHCIEHG-1Caenorhabditis elegans
C414WSCPHCEEHG-1Caenorhabditis elegans
C452HHMEFCRVCKD2Homo sapiens, Mus musculus
C452QNDEFCKICKE1Caenorhabditis elegans
C452ANMDYCRICKE1Caenorhabditis elegans
C452ENA--CQACGE1Arabidopsis thaliana
C452-----C-----1Arabidopsis thaliana
C455EFCRVCKDGGE2Homo sapiens, Mus musculus
C455EFCKICKETEN1Caenorhabditis elegans
C455DYCRICKETSN1Caenorhabditis elegans
C455--CQACGESTN1Arabidopsis thaliana
C455--C--------1Arabidopsis thaliana
C463GGELLCCDTCP2Homo sapiens, Mus musculus
C463TENLLLCDSCV1Caenorhabditis elegans
C463TSNILLCDTCP1Caenorhabditis elegans
C463STNLVSCNTCT1Arabidopsis thaliana
C463-----------1Arabidopsis thaliana
C467LCCDTCPSSYH2Homo sapiens, Mus musculus
C467LLCDSCVCSFH1Caenorhabditis elegans
C467LLCDTCPSSYH1Caenorhabditis elegans
C467VSCNTCTYAFH1Arabidopsis thaliana
C467-----------1Arabidopsis thaliana
C475SYHIHCLNPPL2Homo sapiens, Mus musculus
C475SFHAYCIDPPL1Caenorhabditis elegans
C475SYHAYCIDPPL1Caenorhabditis elegans
C475AFHAKCLVPPL1Arabidopsis thaliana
C475---------PL1Arabidopsis thaliana
C490GE-WLCPRCTC2Homo sapiens, Mus musculus
C490EETWSCPRCET1Caenorhabditis elegans
C490GE-WSCPRCII1Caenorhabditis elegans
C490EN-WRCPECVS1Arabidopsis thaliana
C490-----------1Arabidopsis thaliana
C493WLCPRCTCPAL2Homo sapiens, Mus musculus
C493WSCPRCETVKP1Caenorhabditis elegans
C493WSCPRCIIPEP1Caenorhabditis elegans
C493WRCPECVSPL-1Arabidopsis thaliana
C493-----------1Arabidopsis thaliana
D446LEEEDDHHMEF1Homo sapiens
D446PEEEDDHHMEF1Mus musculus
D446KEEPAKQNDEF1Caenorhabditis elegans
D446EEEPAKANMDY1Caenorhabditis elegans
D446VRTDAKENA--1Arabidopsis thaliana
D446NQD--------1Arabidopsis thaliana
D457CRVCKDGGELL2Homo sapiens, Mus musculus
D457CKICKETENLL1Caenorhabditis elegans
D457CRICKETSNIL1Caenorhabditis elegans
D457CQACGESTNLV1Arabidopsis thaliana
D457C----------1Arabidopsis thaliana
E450DDHHMEFCRVC2Homo sapiens, Mus musculus
E450AKQNDEFCKIC1Caenorhabditis elegans
E450AKANMDYCRIC1Caenorhabditis elegans
E450AKENA--CQAC1Arabidopsis thaliana
E450-------C---1Arabidopsis thaliana
E460CKDGGELLCCD2Homo sapiens, Mus musculus
E460CKETENLLLCD1Caenorhabditis elegans
E460CKETSNILLCD1Caenorhabditis elegans
E460CGESTNLVSCN1Arabidopsis thaliana
E460-----------1Arabidopsis thaliana
F451DHHMEFCRVCK2Homo sapiens, Mus musculus
F451KQNDEFCKICK1Caenorhabditis elegans
F451KANMDYCRICK1Caenorhabditis elegans
F451KENA--CQACG1Arabidopsis thaliana
F451------C----1Arabidopsis thaliana
G458RVCKDGGELLC2Homo sapiens, Mus musculus
G458KICKETENLLL1Caenorhabditis elegans
G458RICKETSNILL1Caenorhabditis elegans
G458QACGESTNLVS1Arabidopsis thaliana
G458-----------1Arabidopsis thaliana
G459VCKDGGELLCC2Homo sapiens, Mus musculus
G459ICKETENLLLC1Caenorhabditis elegans
G459ICKETSNILLC1Caenorhabditis elegans
G459ACGESTNLVSC1Arabidopsis thaliana
G459-----------1Arabidopsis thaliana
G486PEIPNGE-WLC2Homo sapiens, Mus musculus
G486TEVPKEETWSC1Caenorhabditis elegans
G486TEIPEGE-WSC1Caenorhabditis elegans
G486KDASVEN-WRC1Arabidopsis thaliana
G486-----------1Arabidopsis thaliana
H393CPRAYHMVCLD2Homo sapiens, Mus musculus
H393-----------2Arabidopsis thaliana, Arabidopsis thaliana
H393CPRAYHTVCID1Caenorhabditis elegans
H393CTRAYHVACID1Caenorhabditis elegans
H447EEEDDHHMEFC2Homo sapiens, Mus musculus
H447EEPAKQNDEFC1Caenorhabditis elegans
H447EEPAKANMDYC1Caenorhabditis elegans
H447RTDAKENA--C1Arabidopsis thaliana
H447QD--------C1Arabidopsis thaliana
H448EEDDHHMEFCR2Homo sapiens, Mus musculus
H448EPAKQNDEFCK1Caenorhabditis elegans
H448EPAKANMDYCR1Caenorhabditis elegans
H448TDAKENA--CQ1Arabidopsis thaliana
H448D--------C-1Arabidopsis thaliana
H472CPSSYHIHCLN2Homo sapiens, Mus musculus
H472CVCSFHAYCID1Caenorhabditis elegans
H472CPSSYHAYCID1Caenorhabditis elegans
H472CTYAFHAKCLV1Arabidopsis thaliana
H472-----------1Arabidopsis thaliana
I483PPLPEIPNGE-2Homo sapiens, Mus musculus
I483PPLTEVPKEET1Caenorhabditis elegans
I483PPLTEIPEGE-1Caenorhabditis elegans
I483PPLKDASVEN-1Arabidopsis thaliana
I483-PL--------1Arabidopsis thaliana
K456FCRVCKDGGEL2Homo sapiens, Mus musculus
K456FCKICKETENL1Caenorhabditis elegans
K456YCRICKETSNI1Caenorhabditis elegans
K456-CQACGESTNL1Arabidopsis thaliana
K456-C---------1Arabidopsis thaliana
L461KDGGELLCCDT2Homo sapiens, Mus musculus
L461KETENLLLCDS1Caenorhabditis elegans
L461KETSNILLCDT1Caenorhabditis elegans
L461GESTNLVSCNT1Arabidopsis thaliana
L461-----------1Arabidopsis thaliana
L462DGGELLCCDTC2Homo sapiens, Mus musculus
L462ETENLLLCDSC1Caenorhabditis elegans
L462ETSNILLCDTC1Caenorhabditis elegans
L462ESTNLVSCNTC1Arabidopsis thaliana
L462-----------1Arabidopsis thaliana
M449EDDHHMEFCRV2Homo sapiens, Mus musculus
M449PAKQNDEFCKI1Caenorhabditis elegans
M449PAKANMDYCRI1Caenorhabditis elegans
M449DAKENA--CQA1Arabidopsis thaliana
M449--------C--1Arabidopsis thaliana
P484PLPEIPNGE-W2Homo sapiens, Mus musculus
P484PLTEVPKEETW1Caenorhabditis elegans
P484PLTEIPEGE-W1Caenorhabditis elegans
P484PLKDASVEN-W1Arabidopsis thaliana
P484PL---------1Arabidopsis thaliana
T387IILCDTCPRAY2Homo sapiens, Mus musculus
T387-----------2Arabidopsis thaliana, Arabidopsis thaliana
T387LLLCDTCPRAY1Caenorhabditis elegans
T387LMLCDTCTRAY1Caenorhabditis elegans
W488PNGE-WLCPRC2Homo sapiens, Mus musculus
W488PKEETWSCPRC1Caenorhabditis elegans
W488PEGE-WSCPRC1Caenorhabditis elegans
W488SVEN-WRCPEC1Arabidopsis thaliana
W488-----------1Arabidopsis thaliana


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