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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for CHD4

check button Gene summary
Gene informationGene symbol

CHD4

Gene ID

1108

Gene namechromodomain helicase DNA binding protein 4
SynonymsCHD-4|Mi-2b|Mi2-BETA|SIHIWES
Cytomap

12p13.31

Type of geneprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 4ATP-dependent helicase CHD4Mi-2 autoantigen 218 kDa protein
Modification date20180524
UniProtAcc

Q14839

ContextPubMed: CHD4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for CHD4 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for CHD4

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for CHD4

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_89535126680034:6680198:6682239:6682435:6686950:66870136682239:6682435ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1
exon_skip_89541126682239:6682435:6686950:6687083:6687194:66872836686950:6687083ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1
exon_skip_89545126687574:6687712:6688011:6688083:6690209:66903396688011:6688083ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1
exon_skip_89548126690814:6690980:6691302:6691447:6691780:66919146691302:6691447ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1
exon_skip_89550126692192:6692279:6692363:6692541:6696549:66967256692363:6692541ENSG00000111642.10ENST00000540960.1
exon_skip_89551126692192:6692279:6692363:6692544:6696549:66967256692363:6692544ENSG00000111642.10ENST00000357008.2,ENST00000544040.1
exon_skip_89553126697076:6697115:6697463:6697588:6700631:67007496697463:6697588ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1
exon_skip_89554126709700:6709835:6710091:6710219:6710454:67106966710091:6710219ENSG00000111642.10ENST00000309577.6,ENST00000544484.1,ENST00000357008.2,ENST00000544040.1,ENST00000545942.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for CHD4

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_89535126680034:6680198:6682239:6682435:6686950:66870136682239:6682435ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2
exon_skip_89541126682239:6682435:6686950:6687083:6687194:66872836686950:6687083ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2
exon_skip_89545126687574:6687712:6688011:6688083:6690209:66903396688011:6688083ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2
exon_skip_89548126690814:6690980:6691302:6691447:6691780:66919146691302:6691447ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2
exon_skip_89550126692192:6692279:6692363:6692541:6696549:66967256692363:6692541ENSG00000111642.10ENST00000540960.1
exon_skip_89551126692192:6692279:6692363:6692544:6696549:66967256692363:6692544ENSG00000111642.10ENST00000544040.1,ENST00000357008.2
exon_skip_89553126697076:6697115:6697463:6697588:6700631:67007496697463:6697588ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2
exon_skip_89554126709700:6709835:6710091:6710219:6710454:67106966710091:6710219ENSG00000111642.10ENST00000544484.1,ENST00000544040.1,ENST00000309577.6,ENST00000357008.2,ENST00000545942.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for CHD4

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000054404066822396682435Frame-shift
ENST0000054404066869506687083Frame-shift
ENST0000054404066913026691447Frame-shift
ENST0000054404066923636692544Frame-shift
ENST0000054404066974636697588Frame-shift
ENST0000054404067100916710219Frame-shift
ENST0000054404066880116688083In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000054404066822396682435Frame-shift
ENST0000054404066869506687083Frame-shift
ENST0000054404066913026691447Frame-shift
ENST0000054404066923636692544Frame-shift
ENST0000054404066974636697588Frame-shift
ENST0000054404067100916710219Frame-shift
ENST0000054404066880116688083In-frame

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Infer the effects of exon skipping event on protein functional features for CHD4

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000054404065311912668801166880835092516316291653

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000054404065311912668801166880835092516316291653

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q148391629165311912ChainID=PRO_0000080228;Note=Chromodomain-helicase-DNA-binding protein 4
Q148391629165316361636Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733
Q148391629165316431643Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
Q148391629165316471647Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:25772364,ECO:0000244|PubMed:2811273
Q148391629165316431643Modified residueNote=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861
Q148391629165316531653Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:20068231,PMID:23186163,PMID:24275569
Q148391629165316481648Natural variantID=VAR_031675;Note=S->L;Dbxref=dbSNP:rs35512811
Q148391629165315771912RegionNote=Required for interaction with PCNT;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17626165;Dbxref=PMID:17626165


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q148391629165311912ChainID=PRO_0000080228;Note=Chromodomain-helicase-DNA-binding protein 4
Q148391629165316361636Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733
Q148391629165316431643Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
Q148391629165316471647Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25755297,ECO:0000244|PubMed:25772364,ECO:0000244|PubMed:2811273
Q148391629165316431643Modified residueNote=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861
Q148391629165316531653Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:20068231,PMID:23186163,PMID:24275569
Q148391629165316481648Natural variantID=VAR_031675;Note=S->L;Dbxref=dbSNP:rs35512811
Q148391629165315771912RegionNote=Required for interaction with PCNT;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17626165;Dbxref=PMID:17626165


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SNVs in the skipped exons for CHD4

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A3A0-01exon_skip_89545
6688012668808366880326688032Frame_Shift_DelG-p.P1682fs
LIHCTCGA-DD-A3A0-01exon_skip_89550
6692364669254166924126692412Frame_Shift_DelT-p.R1338fs
LIHCTCGA-DD-A3A0-01exon_skip_89551
6692364669254466924126692412Frame_Shift_DelT-p.R1338fs
LIHCTCGA-DD-A3A0-01exon_skip_89554
6710092671021967101166710116Frame_Shift_DelA-p.F301fs
LIHCTCGA-DD-A1EG-01exon_skip_89554
6710092671021967101336710133Frame_Shift_DelT-p.I296fs
LIHCTCGA-G3-A3CJ-01exon_skip_89554
6710092671021967101556710155Frame_Shift_DelG-p.P288fs
SKCMTCGA-EB-A41A-01exon_skip_89554
6710092671021967101076710108Frame_Shift_Ins-Tp.K304fs
SKCMTCGA-EB-A41A-01exon_skip_89554
6710092671021967101076710108Frame_Shift_Ins-Tp.T304fs
BLCATCGA-E7-A541-01exon_skip_89535
6682240668243566823746682374Nonsense_MutationGCp.S1836*
BRCATCGA-A2-A04W-01exon_skip_89545
6688012668808366880606688060Nonsense_MutationCAp.E1645*
SARCTCGA-QC-A7B5-01exon_skip_89550
6692364669254166924336692433Nonsense_MutationGAp.R1331*
SARCTCGA-QC-A7B5-01exon_skip_89551
6692364669254466924336692433Nonsense_MutationGAp.R1331*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
22RV1_PROSTATE6691303669144766914306691430Frame_Shift_DelA-p.F1463fs
SCC90_UPPER_AERODIGESTIVE_TRACT6692364669254466925296692538Frame_Shift_DelCTACCTCCTC-p.EEVE1296fs
SCC90_UPPER_AERODIGESTIVE_TRACT6692364669254166925296692538Frame_Shift_DelCTACCTCCTC-p.EEVE1296fs
IM95_STOMACH6682240668243566822796682279Missense_MutationTCp.M1840V
NO11_CENTRAL_NERVOUS_SYSTEM6682240668243566822906682290Missense_MutationGAp.S1836F
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6682240668243566823826682382Missense_MutationCAp.L1805F
OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6682240668243566823926682392Missense_MutationGTp.A1802D
OPM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6682240668243566823926682392Missense_MutationGTp.A1802D
SNU1040_LARGE_INTESTINE6682240668243566823996682399Missense_MutationGAp.R1800C
JHUEM7_ENDOMETRIUM6686951668708366869906686990Missense_MutationGTp.F1774L
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6686951668708366870736687073Missense_MutationCTp.A1747T
LOXIMVI_SKIN6688012668808366880396688039Missense_MutationGTp.L1652M
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6691303669144766913766691376Missense_MutationCTp.G1481D
TCCSUP_URINARY_TRACT6691303669144766913786691378Missense_MutationATp.D1480E
SW403_LARGE_INTESTINE6692364669254466923986692398Missense_MutationCAp.Q1342H
SW403_LARGE_INTESTINE6692364669254166923986692398Missense_MutationCAp.Q1342H
SNU1040_LARGE_INTESTINE6692364669254466924056692405Missense_MutationCTp.R1340H
SNU1040_LARGE_INTESTINE6692364669254166924056692405Missense_MutationCTp.R1340H
KNS81_CENTRAL_NERVOUS_SYSTEM6692364669254466924686692468Missense_MutationCTp.R1319Q
KNS81_CENTRAL_NERVOUS_SYSTEM6692364669254166924686692468Missense_MutationCTp.R1319Q
KNS81FD_CENTRAL_NERVOUS_SYSTEM6692364669254466924686692468Missense_MutationCTp.R1319Q
KNS81FD_CENTRAL_NERVOUS_SYSTEM6692364669254166924686692468Missense_MutationCTp.R1319Q
SNU1040_LARGE_INTESTINE6692364669254466924686692468Missense_MutationCTp.R1319Q
SNU1040_LARGE_INTESTINE6692364669254166924686692468Missense_MutationCTp.R1319Q
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6692364669254466924936692493Missense_MutationGAp.P1311S
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6692364669254166924936692493Missense_MutationGAp.P1311S
HEC1_ENDOMETRIUM6692364669254466925266692526Missense_MutationGAp.R1300W
HEC1_ENDOMETRIUM6692364669254166925266692526Missense_MutationGAp.R1300W
NCIH2227_LUNG6697464669758866974986697498Missense_MutationTCp.Y1144C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6697464669758866975346697534Missense_MutationCAp.G1132V
HEC108_ENDOMETRIUM6697464669758866975796697579Missense_MutationGCp.A1117G
CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6710092671021967101836710183Missense_MutationCTp.R279H
KYSE70_OESOPHAGUS6710092671021967101876710187Missense_MutationGAp.P278S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CHD4

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CHD4


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CHD4


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RelatedDrugs for CHD4

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CHD4

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
CHD4C0014170Endometrial Neoplasms1CTD_human
CHD4C0036341Schizophrenia1CTD_human