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Editing gene: DDX56 (CAeditome ID:54606)

Gene summary for DDX56

Gene summary

Gene information	Gene symbol	DDX56
	Gene ID	54606
	Gene name	DEAD-box helicase 56
	Synonyms	DDX21\|DDX26\|NOH61
	Cytomap	7p13
	Type of gene	protein-coding
	Description	probable ATP-dependent RNA helicase DDX5661-kd nucleolar helicaseATP-dependent 61 kDa nucleolar RNA helicaseDEAD (Asp-Glu-Ala-Asp) box helicase 56DEAD (Asp-Glu-Ala-Asp) box polypeptide 56DEAD box protein 21DEAD box protein 56DEAD-box RNA helicasen
	Modification date	20210518
	UniProtAcc	Q9NY93
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
DDX56	GO:0005730	Probable ATP-dependent RNA helicase DDX56	0000054

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RNA A-to-I events for DDX56

RNA A-to-I editing events across TCGA 33 cancers data sets based on Ensembl gene isoform structure.

RNA editing frequencies across 33 cancers of gene: ENSG00000136271.9

RNA A-to-I editing events in Cancer.

CAediting_541612(44571152, -), CAediting_541613(44571163, -), CAediting_541614(44571232, -), CAediting_541615(44571234, -), CAediting_541616(44571240, -), CAediting_541617(44571258, -), CAediting_541618(44574097, -), CAediting_541619(44574114, -), CAediting_541620(44574118, -), CAediting_541621(44574147, -), CAediting_541622(44574398, -), CAediting_541623(44574641, -), CAediting_541624(44574651, -), CAediting_541625(44574657, -), CAediting_541626(44574668, -), CAediting_541627(44574675, -), CAediting_541628(44574679, -), CAediting_541629(44574681, -), CAediting_541630(44574684, -), CAediting_541631(44574692, -), CAediting_541632(44574698, -), CAediting_541633(44574723, -), CAediting_541634(44574724, -), CAediting_541635(44574731, -), CAediting_541636(44574737, -), CAediting_541637(44574753, -), CAediting_541638(44574809, -), CAediting_541639(44574855, -), CAediting_541640(44574856, -), CAediting_541641(44574857, -), CAediting_541642(44574858, -), CAediting_541643(44574863, -), CAediting_541644(44574881, -), CAediting_541645(44574885, -), CAediting_541646(44574889, -), CAediting_541647(44574895, -), CAediting_541648(44574903, -), CAediting_541649(44574906, -), CAediting_541650(44574911, -), CAediting_541651(44574912, -), CAediting_541652(44574918, -), CAediting_541653(44574928, -), CAediting_541654(44574931, -), CAediting_541655(44574934, -),

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RNA editing positional annotations for DDX56 using Annovar

Protein coding RNA editing(s).

CAeditome ID

Position

Variant type

ENST

NTchange

AAchange

SIFT_score

Polyphen2_HVAR_score

PROVEAN_pred

Gene structure information of RNA editing(s).

CAeditome ID	Position	Variant type
CAediting_541612	chr7_44571152_-	ncRNA_intronic
CAediting_541613	chr7_44571163_-	ncRNA_intronic
CAediting_541614	chr7_44571232_-	ncRNA_intronic
CAediting_541615	chr7_44571234_-	ncRNA_intronic
CAediting_541616	chr7_44571240_-	ncRNA_intronic
CAediting_541617	chr7_44571258_-	ncRNA_intronic
CAediting_541618	chr7_44574097_-	UTR5
CAediting_541619	chr7_44574114_-	UTR5
CAediting_541620	chr7_44574118_-	UTR5
CAediting_541621	chr7_44574147_-	UTR5
CAediting_541622	chr7_44574398_-	UTR5
CAediting_541623	chr7_44574641_-	UTR5
CAediting_541624	chr7_44574651_-	UTR5
CAediting_541625	chr7_44574657_-	UTR5
CAediting_541626	chr7_44574668_-	UTR5
CAediting_541627	chr7_44574675_-	UTR5
CAediting_541628	chr7_44574679_-	UTR5
CAediting_541629	chr7_44574681_-	UTR5
CAediting_541630	chr7_44574684_-	UTR5
CAediting_541631	chr7_44574692_-	UTR5
CAediting_541632	chr7_44574698_-	UTR5
CAediting_541633	chr7_44574723_-	UTR5
CAediting_541634	chr7_44574724_-	UTR5
CAediting_541635	chr7_44574731_-	UTR5
CAediting_541636	chr7_44574737_-	UTR5
CAediting_541637	chr7_44574753_-	UTR5
CAediting_541638	chr7_44574809_-	UTR5
CAediting_541639	chr7_44574855_-	UTR5
CAediting_541640	chr7_44574856_-	UTR5
CAediting_541641	chr7_44574857_-	UTR5
CAediting_541642	chr7_44574858_-	UTR5
CAediting_541643	chr7_44574863_-	UTR5
CAediting_541644	chr7_44574881_-	UTR5
CAediting_541645	chr7_44574885_-	UTR5
CAediting_541646	chr7_44574889_-	UTR5
CAediting_541647	chr7_44574895_-	UTR5
CAediting_541648	chr7_44574903_-	UTR5
CAediting_541649	chr7_44574906_-	UTR5
CAediting_541650	chr7_44574911_-	UTR5
CAediting_541651	chr7_44574912_-	UTR5
CAediting_541652	chr7_44574918_-	UTR5
CAediting_541653	chr7_44574928_-	UTR5
CAediting_541654	chr7_44574931_-	UTR5
CAediting_541655	chr7_44574934_-	UTR5

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_541612	chr7_44571152_-	SINE	Alu	AluSq2
CAediting_541613	chr7_44571163_-	SINE	Alu	AluSq2
CAediting_541614	chr7_44571232_-	SINE	Alu	AluSq2
CAediting_541615	chr7_44571234_-	SINE	Alu	AluSq2
CAediting_541616	chr7_44571240_-	SINE	Alu	AluSq2
CAediting_541617	chr7_44571258_-	SINE	Alu	AluSq2
CAediting_541623	chr7_44574641_-	SINE	Alu	AluJo
CAediting_541624	chr7_44574651_-	SINE	Alu	AluJo
CAediting_541625	chr7_44574657_-	SINE	Alu	AluJo
CAediting_541626	chr7_44574668_-	SINE	Alu	AluJo
CAediting_541627	chr7_44574675_-	SINE	Alu	AluJo
CAediting_541628	chr7_44574679_-	SINE	Alu	AluJo
CAediting_541629	chr7_44574681_-	SINE	Alu	AluJo
CAediting_541630	chr7_44574684_-	SINE	Alu	AluJo
CAediting_541631	chr7_44574692_-	SINE	Alu	AluJo
CAediting_541632	chr7_44574698_-	SINE	Alu	AluJo
CAediting_541633	chr7_44574723_-	SINE	Alu	AluJo
CAediting_541634	chr7_44574724_-	SINE	Alu	AluJo
CAediting_541635	chr7_44574731_-	SINE	Alu	AluJo
CAediting_541636	chr7_44574737_-	SINE	Alu	AluJo
CAediting_541637	chr7_44574753_-	SINE	Alu	AluJo
CAediting_541638	chr7_44574809_-	SINE	Alu	AluJo
CAediting_541639	chr7_44574855_-	SINE	Alu	AluJo
CAediting_541640	chr7_44574856_-	SINE	Alu	AluJo
CAediting_541641	chr7_44574857_-	SINE	Alu	AluJo
CAediting_541642	chr7_44574858_-	SINE	Alu	AluJo
CAediting_541643	chr7_44574863_-	SINE	Alu	AluJo
CAediting_541644	chr7_44574881_-	SINE	Alu	AluJo
CAediting_541645	chr7_44574885_-	SINE	Alu	AluJo
CAediting_541646	chr7_44574889_-	SINE	Alu	AluJo
CAediting_541647	chr7_44574895_-	SINE	Alu	AluJo
CAediting_541648	chr7_44574903_-	SINE	Alu	AluJo
CAediting_541649	chr7_44574906_-	SINE	Alu	AluJo
CAediting_541650	chr7_44574911_-	SINE	Alu	AluJo
CAediting_541651	chr7_44574912_-	SINE	Alu	AluJo
CAediting_541652	chr7_44574918_-	SINE	Alu	AluJo
CAediting_541653	chr7_44574928_-	SINE	Alu	AluJo
CAediting_541654	chr7_44574931_-	SINE	Alu	AluJo
CAediting_541655	chr7_44574934_-	SINE	Alu	AluJo

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RNA A-to-I editing events in the alternative splicing sites for DDX56

RNA A-to-I editing(s) in the alternative splicing sites.

AStype

CAeditomID

Editing position

AS position

AS direction

Exonic location

Wildtype sequence

Wildtype splicing strength

RNA edited sequence

RNA edited splicing strength

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000136271.9.DDX56.

Correlation between RNA A-to-I editing and PSI for ENSG00000136271.9.DDX56.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for DDX56

Differential gene expressions between RNA A-to-I edited and non-edited tumor samples.
* The grey color means N/A.

Correlation between RNA A-to-I editing and gene expression.

- Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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Protein coding region RNA A-to-I editings for DDX56

- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.

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The effects of the RNA editing to the miRNA binding sites for DDX56

**If you are searching a miRNA gene with RNA editing events in its seed regions, please see the search pages of miRNA targets to discover the effects of this RNA editing event to miRNA regulations. For more information, please check the files in the Download page.

RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs lost binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_573001	chr7_92204086_-	ENSG00000136271.9	ENST00000446987	hsa-miR-1285-5p	44571663	44571669	7mer-m8	44571662	44571682	140	-16.33
CAediting_1229415	chr17_67471547_+	ENSG00000136271.9	ENST00000415758	hsa-miR-548aa	44572600	44572606	7mer-m8	44572599	44572623	142	-7.23
CAediting_573001	chr7_92204086_-	ENSG00000136271.9	ENST00000415758	hsa-miR-1285-5p	44571663	44571669	7mer-m8	44571662	44571682	140	-16.33

RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for DDX56

- RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.

ENST	ENST type	RNA structure without RNA A-to-I editing.	RNA structure with RNA A-to-I editing.
ENST00000421223.4	nonsense_mediated_decay

RNA A-to-I editing in RNA structures for Minimum free energy (MFE).

CAeditom_ID	ENST	Editing_Position	MFE_withoneAI	MFE_withoutAI	MFE_withmultipleAI
CAediting_541618	ENST00000421223.4	chr7_44574097_-	-1163.00	-1163.00	-1211.40
CAediting_541619	ENST00000421223.4	chr7_44574114_-	-1163.00	-1163.00	-1211.40
CAediting_541620	ENST00000421223.4	chr7_44574118_-	-1164.00	-1163.00	-1211.40
CAediting_541621	ENST00000421223.4	chr7_44574147_-	-1166.80	-1163.00	-1211.40
CAediting_541622	ENST00000421223.4	chr7_44574398_-	-1168.20	-1163.00	-1211.40
CAediting_541623	ENST00000421223.4	chr7_44574641_-	-1162.30	-1163.00	-1211.40
CAediting_541624	ENST00000421223.4	chr7_44574651_-	-1168.50	-1163.00	-1211.40
CAediting_541625	ENST00000421223.4	chr7_44574657_-	-1166.90	-1163.00	-1211.40
CAediting_541626	ENST00000421223.4	chr7_44574668_-	-1163.60	-1163.00	-1211.40
CAediting_541627	ENST00000421223.4	chr7_44574675_-	-1162.70	-1163.00	-1211.40
CAediting_541628	ENST00000421223.4	chr7_44574679_-	-1163.60	-1163.00	-1211.40
CAediting_541629	ENST00000421223.4	chr7_44574681_-	-1163.50	-1163.00	-1211.40
CAediting_541630	ENST00000421223.4	chr7_44574684_-	-1162.30	-1163.00	-1211.40
CAediting_541631	ENST00000421223.4	chr7_44574692_-	-1163.00	-1163.00	-1211.40
CAediting_541632	ENST00000421223.4	chr7_44574698_-	-1161.70	-1163.00	-1211.40
CAediting_541633	ENST00000421223.4	chr7_44574723_-	-1163.00	-1163.00	-1211.40
CAediting_541634	ENST00000421223.4	chr7_44574724_-	-1163.40	-1163.00	-1211.40
CAediting_541635	ENST00000421223.4	chr7_44574731_-	-1163.90	-1163.00	-1211.40
CAediting_541636	ENST00000421223.4	chr7_44574737_-	-1167.50	-1163.00	-1211.40
CAediting_541637	ENST00000421223.4	chr7_44574753_-	-1164.30	-1163.00	-1211.40
CAediting_541638	ENST00000421223.4	chr7_44574809_-	-1164.30	-1163.00	-1211.40
CAediting_541639	ENST00000421223.4	chr7_44574855_-	-1163.00	-1163.00	-1211.40
CAediting_541640	ENST00000421223.4	chr7_44574856_-	-1163.00	-1163.00	-1211.40
CAediting_541641	ENST00000421223.4	chr7_44574857_-	-1163.00	-1163.00	-1211.40
CAediting_541642	ENST00000421223.4	chr7_44574858_-	-1163.10	-1163.00	-1211.40
CAediting_541643	ENST00000421223.4	chr7_44574863_-	-1163.80	-1163.00	-1211.40
CAediting_541644	ENST00000421223.4	chr7_44574881_-	-1162.30	-1163.00	-1211.40
CAediting_541645	ENST00000421223.4	chr7_44574885_-	-1164.60	-1163.00	-1211.40
CAediting_541646	ENST00000421223.4	chr7_44574889_-	-1164.20	-1163.00	-1211.40
CAediting_541647	ENST00000421223.4	chr7_44574895_-	-1161.80	-1163.00	-1211.40
CAediting_541648	ENST00000421223.4	chr7_44574903_-	-1163.00	-1163.00	-1211.40
CAediting_541649	ENST00000421223.4	chr7_44574906_-	-1167.20	-1163.00	-1211.40
CAediting_541650	ENST00000421223.4	chr7_44574911_-	-1163.30	-1163.00	-1211.40
CAediting_541651	ENST00000421223.4	chr7_44574912_-	-1163.00	-1163.00	-1211.40
CAediting_541652	ENST00000421223.4	chr7_44574918_-	-1163.90	-1163.00	-1211.40
CAediting_541653	ENST00000421223.4	chr7_44574928_-	-1164.00	-1163.00	-1211.40
CAediting_541654	ENST00000421223.4	chr7_44574931_-	-1162.10	-1163.00	-1211.40
CAediting_541655	ENST00000421223.4	chr7_44574934_-	-1164.50	-1163.00	-1211.40

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Relation with ADAR for DDX56

Correlation between ADAR gene expression and RNA editing frequency

Cancer	CAeditomID	position	ADAR1 (p-val)	ADAR1 (coeff.)	ADAR2 (p-val)	ADAR2 (coeff.)	ADAR3 (p-val)	ADAR3 (coeff.)
STAD	CAediting_541632	chr7_44574698_-	0.0139020688956733	0.221293703154645	.	.	.	.
UCEC	CAediting_541632	chr7_44574698_-	0.0178093053189563	0.30007024519657	.	.	.	.
ESCA	CAediting_541632	chr7_44574698_-	.	.	0.0267610422316739	0.241701043488188	.	.
LGG	CAediting_541633	chr7_44574723_-	.	.	.	.	8.59276156621064e-07	0.297964671769539
PRAD	CAediting_541633	chr7_44574723_-	0.00187615721017324	0.236124483201118	.	.	.	.
LAML	CAediting_541633	chr7_44574723_-	0.00564043725665291	0.253339553861159	.	.	.	.
OV	CAediting_541633	chr7_44574723_-	0.0465133985070456	0.14858880308658	.	.	.	.
SARC	CAediting_541633	chr7_44574723_-	0.00205191752520939	0.406861369783072	.	.	.	.
TGCT	CAediting_541633	chr7_44574723_-	0.000744525175201566	0.356850503896653	.	.	.	.
THYM	CAediting_541633	chr7_44574723_-	.	.	.	.	0.0255061298434839	0.290704815683142
LUAD	CAediting_541640	chr7_44574856_-	0.0401708122766819	0.272659803132906	.	.	0.0020623183287308	0.399793866192262

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Relation with cancer stages for DDX56

Correlation between Cancer stages and RNA editing frequency

Cancer	Stage_type	CAeditomID	position	P-val	Coeff.
BRCA	pathologic_stage	CAediting_541633	chr7_44574723_-	0.0277371373757852	-0.151906518942991
KIRC	pathologic_stage	CAediting_541633	chr7_44574723_-	0.00135782228155578	0.203968317880096
KIRP	pathologic_stage	CAediting_541632	chr7_44574698_-	0.0209212186437595	0.244524282784306
LUAD	pathologic_stage	CAediting_541633	chr7_44574723_-	0.0450713665994153	0.170270291222585
LUSC	pathologic_stage	CAediting_541633	chr7_44574723_-	0.0025032034145122	0.267058780067602
OV	clinical_stage	CAediting_541632	chr7_44574698_-	0.0380498007501274	0.189621637143006

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Relation with survival for DDX56

Correlation between RNA editing and survival

Cancer	CAeditomID	position	KMpvalue	Coxpvalue	CoxHR
LGG	CAediting_541632	chr7_44574698_-	0.0195984235058416	0.0128939	52.5072
SARC	CAediting_541633	chr7_44574723_-	0.0115114911022064	0.0499036	26.1795

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RelatedDrugs for DDX56

Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for DDX56

Diseases associated with this gene.
(DisGeNet 7.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	RNA A-to-I events
	Differntial gene expression between RNA A-to-I edited tumor samples versus normal samples
	Protein coding region RNA A-to-I editings
	The effects of the RNA editing to the miRNA binding sites
	The effects of the RNA editing to the stability of the RNA structures
	Relation with ADAR
	Relation with cancer stages
	Relation with survival state
	Related drugs with this gene
	Related diseases with this gene