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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 TNFRSF14 |
 Gene summary |
| Gene information | Gene symbol | TNFRSF14 | Gene ID | 8764 |
| Gene name | TNF receptor superfamily member 14 | |
| Synonyms | ATAR|CD270|HVEA|HVEM|LIGHTR|TR2 | |
| Cytomap | 1p36.32 | |
| Type of gene | protein-coding | |
| Description | tumor necrosis factor receptor superfamily member 14CD40-like proteinherpes virus entry mediator Atumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)tumor necrosis factor receptor-like gene2 | |
| Modification date | 20200313 | |
| UniProtAcc | Q92956, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| TNFRSF14 | GO:0031295 | T cell costimulation | 10754304 |
| TNFRSF14 | GO:1905675 | negative regulation of adaptive immune memory response | 18193050 |
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RNA A-to-I events for TNFRSF14 |
| 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. |
| 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_87629(2561799, +), ADediting_87630(2561803, +), ADediting_87631(2561806, +), ADediting_87632(2561807, +), ADediting_1518610(2561800, +), |
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RNA editing positional annotations for TNFRSF14 using Annovar |
| Protein coding RNA editing(s). |
| ADeditome ID | Position | Variant type | ENST | NTchange | AAchange | SIFT_score | Polyphen2_HVAR_score | PROVEAN_pred |
| ADediting_1518610 | chr1_2561800_+ | nonsynonymous SNV | ENST00000355716.4 | c.A679G | p.R227G | 0.017 | 0.206 | -1.55 |
| ADediting_1518610 | chr1_2561800_+ | nonsynonymous SNV | ENST00000435221.6 | c.A679G | p.R227G | 0.017 | 0.206 | -1.55 |
| ADediting_1518610 | chr1_2561800_+ | nonsynonymous SNV | ENST00000451778.5 | c.A679G | p.R227G | 0.017 | 0.206 | -1.55 |
| ADediting_1518610 | chr1_2561800_+ | nonsynonymous SNV | ENST00000434817.5 | c.A679G | p.R227G | 0.017 | 0.206 | -1.55 |
| ADediting_87629 | chr1_2561799_+ | synonymous SNV | ENST00000355716.4 | c.A678G | p.K226K | . | . | . |
| ADediting_87629 | chr1_2561799_+ | synonymous SNV | ENST00000435221.6 | c.A678G | p.K226K | . | . | . |
| ADediting_87629 | chr1_2561799_+ | synonymous SNV | ENST00000451778.5 | c.A678G | p.K226K | . | . | . |
| ADediting_87629 | chr1_2561799_+ | synonymous SNV | ENST00000434817.5 | c.A678G | p.K226K | . | . | . |
| ADediting_87630 | chr1_2561803_+ | nonsynonymous SNV | ENST00000355716.4 | c.A682G | p.R228G | 0.058 | 0.354 | -1.71 |
| ADediting_87630 | chr1_2561803_+ | nonsynonymous SNV | ENST00000435221.6 | c.A682G | p.R228G | 0.058 | 0.354 | -1.71 |
| ADediting_87630 | chr1_2561803_+ | nonsynonymous SNV | ENST00000451778.5 | c.A682G | p.R228G | 0.058 | 0.354 | -1.71 |
| ADediting_87630 | chr1_2561803_+ | nonsynonymous SNV | ENST00000434817.5 | c.A682G | p.R228G | 0.058 | 0.354 | -1.71 |
| ADediting_87631 | chr1_2561806_+ | nonsynonymous SNV | ENST00000355716.4 | c.A685G | p.K229E | 0.025 | 0.057 | -0.63 |
| ADediting_87631 | chr1_2561806_+ | nonsynonymous SNV | ENST00000435221.6 | c.A685G | p.K229E | 0.025 | 0.057 | -0.63 |
| ADediting_87631 | chr1_2561806_+ | nonsynonymous SNV | ENST00000451778.5 | c.A685G | p.K229E | 0.025 | 0.057 | -0.63 |
| ADediting_87631 | chr1_2561806_+ | nonsynonymous SNV | ENST00000434817.5 | c.A685G | p.K229E | 0.025 | 0.057 | -0.63 |
| ADediting_87632 | chr1_2561807_+ | nonsynonymous SNV | ENST00000355716.4 | c.A686G | p.K229R | 0.363 | 0.0 | -0.2 |
| ADediting_87632 | chr1_2561807_+ | nonsynonymous SNV | ENST00000435221.6 | c.A686G | p.K229R | 0.363 | 0.0 | -0.2 |
| ADediting_87632 | chr1_2561807_+ | nonsynonymous SNV | ENST00000451778.5 | c.A686G | p.K229R | 0.363 | 0.0 | -0.2 |
| ADediting_87632 | chr1_2561807_+ | nonsynonymous SNV | ENST00000434817.5 | c.A686G | p.K229R | 0.363 | 0.0 | -0.2 |
| Gene structure information of RNA editing(s). |
| ADeditome ID | Position | Variant type |
| ADediting_87629 | chr1_2561799_+ | exonic |
| ADediting_87630 | chr1_2561803_+ | exonic |
| ADediting_87631 | chr1_2561806_+ | exonic |
| ADediting_87632 | chr1_2561807_+ | exonic |
| ADediting_1518610 | chr1_2561800_+ | exonic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
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RNA A-to-I editing events in the alternative splicing sites for TNFRSF14 |
| 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 TNFRSF14 |
| 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. |
| - 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. |
| ADeditome ID | Chr | Positoing | Skipped exon | ENSG | ENSTs |
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Protein coding region RNA A-to-I editings for TNFRSF14 |
| - 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 TNFRSF14 |
| 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 |
| ADediting_1471003 | chr9_63819626_+ | ENSG00000157873.17 | ENST00000355716.4 | TNFRSF14-201 | hsa-miR-4477b | chr1 | 2563821 | 2563828 | 8mer-1a | 2563807 | 2563828 | 150 | -9.96 |
| ADediting_496066 | chr15_66496985_- | ENSG00000157873.17 | ENST00000355716.4 | TNFRSF14-201 | hsa-miR-4512 | chr1 | 2563642 | 2563648 | 7mer-m8 | 2563626 | 2563649 | 142 | -27.71 |
| 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_291761 | chr11_93733708_- | ENSG00000157873.17 | ENST00000355716.4 | TNFRSF14-201 | hsa-miR-1304-3p | chr1 | 2563469 | 2563475 | 7mer-m8 | 2563457 | 2563476 | 143 | -18.16 |
| Differentially expressed gene-miRNA network |
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The effects of the RNA editing to the stability of the RNA structures for TNFRSF14 |
| - 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. |
| ENST00000451778.5 | protein_coding |  |  |
| ENST00000355716.4 | protein_coding |  |  |
| ENST00000482602.5 | protein_coding |  |  |
| ENST00000434817.5 | protein_coding |  |  |
| ENST00000435221.6 | protein_coding |  |  |
| ENST00000480305.1 | lncRNA |  |  |
| 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 |
| ADediting_87629 | ENST00000451778.5 | chr1_2561799_+ | 811 | -347.00 | -345.40 | -351.50 |
| ADediting_1518610 | ENST00000451778.5 | chr1_2561800_+ | 812 | -345.10 | -345.40 | -351.50 |
| ADediting_87630 | ENST00000451778.5 | chr1_2561803_+ | 815 | -347.20 | -345.40 | -351.50 |
| ADediting_87631 | ENST00000451778.5 | chr1_2561806_+ | 818 | -349.40 | -345.40 | -351.50 |
| ADediting_87632 | ENST00000451778.5 | chr1_2561807_+ | 819 | -348.80 | -345.40 | -351.50 |
| ADediting_87629 | ENST00000355716.4 | chr1_2561799_+ | 977 | -727.70 | -726.70 | -734.90 |
| ADediting_1518610 | ENST00000355716.4 | chr1_2561800_+ | 978 | -727.10 | -726.70 | -734.90 |
| ADediting_87630 | ENST00000355716.4 | chr1_2561803_+ | 981 | -727.80 | -726.70 | -734.90 |
| ADediting_87631 | ENST00000355716.4 | chr1_2561806_+ | 984 | -728.80 | -726.70 | -734.90 |
| ADediting_87632 | ENST00000355716.4 | chr1_2561807_+ | 985 | -730.30 | -726.70 | -734.90 |
| ADediting_87629 | ENST00000482602.5 | chr1_2561799_+ | 56 | -186.70 | -185.70 | -189.90 |
| ADediting_1518610 | ENST00000482602.5 | chr1_2561800_+ | 57 | -186.20 | -185.70 | -189.90 |
| ADediting_87630 | ENST00000482602.5 | chr1_2561803_+ | 60 | -185.70 | -185.70 | -189.90 |
| ADediting_87631 | ENST00000482602.5 | chr1_2561806_+ | 63 | -187.10 | -185.70 | -189.90 |
| ADediting_87632 | ENST00000482602.5 | chr1_2561807_+ | 64 | -189.30 | -185.70 | -189.90 |
| ADediting_87629 | ENST00000434817.5 | chr1_2561799_+ | 818 | -357.60 | -357.60 | -365.40 |
| ADediting_1518610 | ENST00000434817.5 | chr1_2561800_+ | 819 | -357.60 | -357.60 | -365.40 |
| ADediting_87630 | ENST00000434817.5 | chr1_2561803_+ | 822 | -357.60 | -357.60 | -365.40 |
| ADediting_87631 | ENST00000434817.5 | chr1_2561806_+ | 825 | -357.60 | -357.60 | -365.40 |
| ADediting_87632 | ENST00000434817.5 | chr1_2561807_+ | 826 | -358.20 | -357.60 | -365.40 |
| ADediting_87629 | ENST00000435221.6 | chr1_2561799_+ | 1209 | -545.90 | -544.90 | -553.40 |
| ADediting_1518610 | ENST00000435221.6 | chr1_2561800_+ | 1210 | -545.90 | -544.90 | -553.40 |
| ADediting_87630 | ENST00000435221.6 | chr1_2561803_+ | 1213 | -545.30 | -544.90 | -553.40 |
| ADediting_87631 | ENST00000435221.6 | chr1_2561806_+ | 1216 | -546.30 | -544.90 | -553.40 |
| ADediting_87632 | ENST00000435221.6 | chr1_2561807_+ | 1217 | -548.50 | -544.90 | -553.40 |
| RNA A-to-I editing in lncRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| ADediting_87630 | ENST00000480305.1 | chr1_2561803_+ | 3 | -224.80 | -224.80 | -227.70 |
| ADediting_87631 | ENST00000480305.1 | chr1_2561806_+ | 6 | -229.10 | -224.80 | -227.70 |
| ADediting_87632 | ENST00000480305.1 | chr1_2561807_+ | 7 | -224.80 | -224.80 | -227.70 |
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Relation with ADAR for TNFRSF14 |
| 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.) |
| 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 | 1.46396708417579e-14 | 0.41829801809365 | 3.87467903312071e-19 | 0.47843141249236 | 1.89559058876857e-21 | 0.504804305042974 |
| AC | 6.94669436867447e-23 | 0.569396538667255 | 2.3137023045661e-12 | 0.424575428086195 | 2.29806043742052e-21 | 0.552302882503226 |
| PCC | 2.53981958593114e-09 | 0.414350919831423 | 4.9396524205363e-08 | 0.382036283404913 | 2.39305250648685e-06 | 0.333670298676207 |
| FP | 9.54374146951355e-09 | 0.413624390194758 | 0.000105100059329465 | 0.286603169844323 | 1.41077468501237e-06 | 0.352354510535269 |
| IFG | 0.00595837599957701 | 0.534096699845497 | 0.00166958577154623 | 0.595929526105828 | 0.118963806568334 | 0.31994600204052 |
| STG | 0.149321603517973 | 0.158706654084482 | 0.422012210687951 | -0.0887643187482981 | 1.7328378385653e-05 | 0.450203189868771 |
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Relation with AD stages for TNFRSF14 |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
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RelatedDrugs for TNFRSF14 |
| 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 TNFRSF14 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| TNFRSF14 | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
| TNFRSF14 | C0007570 | Celiac Disease | 1 | CTD_human |
| TNFRSF14 | C0085742 | Injuries, Acute Brain | 1 | CTD_human |
| TNFRSF14 | C0270611 | Brain Injuries | 1 | CTD_human |
| TNFRSF14 | C0272945 | Brain Lacerations | 1 | CTD_human |
| TNFRSF14 | C0452047 | Brain Injuries, Focal | 1 | CTD_human |
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