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| Differntial gene expression between RNA A-to-I edited versus non-edited samples |
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| The effects of the RNA editing to the stability of the RNA structures |
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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 | 20200313 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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RNA A-to-I events for DDX56 |
| RNA A-to-I editing events in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure. * This pie chart shows the number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
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| RNA editing frequencies across three data sets. |
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| The number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
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| RNA A-to-I editing events in AD. |
| ADediting_1333076(44571212, -), ADediting_1333077(44571240, -), ADediting_1333078(44571252, -), ADediting_1333079(44571257, -), ADediting_1333080(44574398, -), ADediting_1333081(44574651, -), ADediting_1333082(44574675, -), ADediting_1333083(44574681, -), ADediting_1333084(44574684, -), ADediting_1333085(44574698, -), ADediting_1333086(44574723, -), ADediting_1333087(44574724, -), ADediting_1333088(44574855, -), ADediting_1333089(44574856, -), ADediting_1333090(44574857, -), ADediting_1333091(44574858, -), ADediting_1333092(44574866, -), ADediting_1333093(44574881, -), ADediting_1333094(44574885, -), ADediting_1333095(44574895, -), ADediting_1333096(44574911, -), ADediting_1333097(44574912, -), ADediting_1333098(44574918, -), ADediting_1333099(44574928, -), ADediting_1333100(44574934, -), ADediting_1587539(44571271, -), ADediting_1587540(44571295, -), ADediting_1587541(44574903, -), |
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RNA editing positional annotations for DDX56 using Annovar |
| Protein coding RNA editing(s). |
| ADeditome ID | Position | Variant type | ENST | NTchange | AAchange | SIFT_score | Polyphen2_HVAR_score | PROVEAN_pred |
| Gene structure information of RNA editing(s). |
| ADeditome ID | Position | Variant type |
| ADediting_1333076 | chr7_44571212_- | intronic |
| ADediting_1333077 | chr7_44571240_- | intronic |
| ADediting_1333078 | chr7_44571252_- | intronic |
| ADediting_1333079 | chr7_44571257_- | intronic |
| ADediting_1333080 | chr7_44574398_- | UTR5 |
| ADediting_1333081 | chr7_44574651_- | UTR5 |
| ADediting_1333082 | chr7_44574675_- | UTR5 |
| ADediting_1333083 | chr7_44574681_- | UTR5 |
| ADediting_1333084 | chr7_44574684_- | UTR5 |
| ADediting_1333085 | chr7_44574698_- | UTR5 |
| ADediting_1333086 | chr7_44574723_- | UTR5 |
| ADediting_1333087 | chr7_44574724_- | UTR5 |
| ADediting_1333088 | chr7_44574855_- | UTR5 |
| ADediting_1333089 | chr7_44574856_- | UTR5 |
| ADediting_1333090 | chr7_44574857_- | UTR5 |
| ADediting_1333091 | chr7_44574858_- | UTR5 |
| ADediting_1333092 | chr7_44574866_- | UTR5 |
| ADediting_1333093 | chr7_44574881_- | UTR5 |
| ADediting_1333094 | chr7_44574885_- | UTR5 |
| ADediting_1333095 | chr7_44574895_- | UTR5 |
| ADediting_1333096 | chr7_44574911_- | UTR5 |
| ADediting_1333097 | chr7_44574912_- | UTR5 |
| ADediting_1333098 | chr7_44574918_- | UTR5 |
| ADediting_1333099 | chr7_44574928_- | UTR5 |
| ADediting_1333100 | chr7_44574934_- | UTR5 |
| ADediting_1587539 | chr7_44571271_- | intronic |
| ADediting_1587540 | chr7_44571295_- | intronic |
| ADediting_1587541 | chr7_44574903_- | UTR5 |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_1333076 | chr7_44571212_- | SINE | Alu | Name=AluSq2 |
| ADediting_1333077 | chr7_44571240_- | SINE | Alu | Name=AluSq2 |
| ADediting_1333078 | chr7_44571252_- | SINE | Alu | Name=AluSq2 |
| ADediting_1333079 | chr7_44571257_- | SINE | Alu | Name=AluSq2 |
| ADediting_1333081 | chr7_44574651_- | SINE | Alu | Name=AluJo |
| ADediting_1333082 | chr7_44574675_- | SINE | Alu | Name=AluJo |
| ADediting_1333083 | chr7_44574681_- | SINE | Alu | Name=AluJo |
| ADediting_1333084 | chr7_44574684_- | SINE | Alu | Name=AluJo |
| ADediting_1333085 | chr7_44574698_- | SINE | Alu | Name=AluJo |
| ADediting_1333086 | chr7_44574723_- | SINE | Alu | Name=AluJo |
| ADediting_1333087 | chr7_44574724_- | SINE | Alu | Name=AluJo |
| ADediting_1333088 | chr7_44574855_- | SINE | Alu | Name=AluJo |
| ADediting_1333089 | chr7_44574856_- | SINE | Alu | Name=AluJo |
| ADediting_1333090 | chr7_44574857_- | SINE | Alu | Name=AluJo |
| ADediting_1333091 | chr7_44574858_- | SINE | Alu | Name=AluJo |
| ADediting_1333092 | chr7_44574866_- | SINE | Alu | Name=AluJo |
| ADediting_1333093 | chr7_44574881_- | SINE | Alu | Name=AluJo |
| ADediting_1333094 | chr7_44574885_- | SINE | Alu | Name=AluJo |
| ADediting_1333095 | chr7_44574895_- | SINE | Alu | Name=AluJo |
| ADediting_1333096 | chr7_44574911_- | SINE | Alu | Name=AluJo |
| ADediting_1333097 | chr7_44574912_- | SINE | Alu | Name=AluJo |
| ADediting_1333098 | chr7_44574918_- | SINE | Alu | Name=AluJo |
| ADediting_1333099 | chr7_44574928_- | SINE | Alu | Name=AluJo |
| ADediting_1333100 | chr7_44574934_- | SINE | Alu | Name=AluJo |
| ADediting_1587539 | chr7_44571271_- | SINE | Alu | Name=AluSq2 |
| ADediting_1587540 | chr7_44571295_- | SINE | Alu | Name=AluSq2 |
| ADediting_1587541 | chr7_44574903_- | SINE | Alu | Name=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 | ADeditomID | Editing position | AS position | AS direction | Exonic location | Wildtype sequence | Wildtype splicing strength | RNA edited sequence | RNA edited splicing strength |
| Differential pencent of spliced in (PSI) between RNA A-to-I edited and non-edited samples |
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Differntial gene expression between RNA A-to-I edited versus non-edited samples for DDX56 |
| Distribution of the averaged gene expression in AD and control with or without RNA A-to-I editing event. * The grey color means N/A. |
| Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event. |
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| - 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. |
| - Differentially expressed transcript 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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| ADeditome ID | Chr | Positoing | Skipped exon | ENSG | ENSTs |
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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 |
| RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | 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. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in lncRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in lncRNA lost miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs gained binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs lost binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | 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. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_496066 | chr15_66496985_- | ENSG00000136271.10 | ENST00000448192.1 | DDX56-207 | hsa-miR-4512 | chr7 | 44566251 | 44566257 | 7mer-m8 | 44566250 | 44566272 | 141 | -21.19 |
| 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. |
| RNA A-to-I editing in miRNA. |
| ADeditom_ID | ENST | mir_ID | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in mRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in lncRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
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Relation with ADAR for DDX56 |
| Correlation between ADAR gene expression and RNA editing frequency |
| Tissue | ADeditomID | position | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| DLPFC | ADediting_1333080 | chr7_44574398_- | 6.18637581024289e-06 | 0.253531720904927 | 3.99923189720973e-09 | 0.326326820003165 | 0.413249355993778 | 0.0466331042912912 |
| CER | ADediting_1333084 | chr7_44574684_- | 0.000126877920930308 | 0.307858231761545 | 1.0842485740992e-05 | 0.350687978956081 | 0.350548527875081 | 0.0767516230227056 |
| TCX | ADediting_1333086 | chr7_44574723_- | 1.78146571072823e-05 | 0.342538143452626 | 0.0725400228816265 | 0.147051450966934 | 0.00612443849447971 | 0.222847951392291 |
| CER | ADediting_1333089 | chr7_44574856_- | 0.000154684823004017 | 0.304110097745272 | 2.00236714050003e-06 | 0.376843261234154 | 0.0126793809564949 | 0.203097233273678 |
| CER | ADediting_1333094 | chr7_44574885_- | 0.00638139671282744 | 0.221775409714085 | 8.49910503779735e-09 | 0.448674206195806 | 0.276789412777413 | 0.0893686939233706 |
| Correlation between ADAR gene expression and this gene's expression |
| Tissue | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| DLPFC | 5.94083874357025e-20 | 0.487989572362488 | 8.01792470757263e-36 | 0.630936827472869 | 0.000509240853040826 | 0.196284028784995 |
| AC | 1.08094238330851e-75 | 0.863529808618987 | 1.65734430888774e-54 | 0.789537381049137 | 1.49355463274323e-16 | 0.490686522933214 |
| PCC | 9.78086844786905e-15 | 0.52188830431804 | 1.1553020656012e-17 | 0.56735038466488 | 0.110177259480219 | 0.115954520559314 |
| CER | 2.72936352075539e-07 | -0.405036581585603 | 0.000963537004716569 | -0.266850294790197 | 0.00601532068819048 | -0.223315584796054 |
| TCX | 0.0790308119903683 | 0.143860894729076 | 3.09144549082991e-06 | 0.37033405732691 | 0.132045242028363 | 0.12353325700261 |
| FP | 4.78004739952105e-34 | 0.754720601136632 | 3.06482692376721e-38 | 0.783685781261894 | 7.35007500918711e-09 | 0.416509450433644 |
| IFG | 9.516797457543e-10 | 0.899691643574816 | 6.00403341588487e-07 | 0.817724776459919 | 0.189755702923615 | 0.271197575647019 |
| PG | 0.000137669351471857 | 0.275945930978105 | 3.33260690833257e-07 | 0.363765778913319 | 0.0509424680694619 | 0.143351246867593 |
| STG | 8.71608074295671e-24 | 0.84294151318189 | 3.75928168817685e-12 | 0.66832857036309 | 0.0544360238007257 | 0.210649894347574 |
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Relation with AD stages for DDX56 |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| CER | ADediting_1333079 | chr7_44571257_- | 0.00143125332133593 | 0.303069224460311 |
| TCX | ADediting_1333085 | chr7_44574698_- | 0.00101847526458218 | 0.31468716865164 |
| TCX | ADediting_1333086 | chr7_44574723_- | 2.03887142192673e-05 | 0.401068989265359 |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
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RelatedDrugs for DDX56 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| 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 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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