|
||||||
|
 | |
| |
| Differntial gene expression between RNA A-to-I edited versus non-edited samples |
| |
| |
| The effects of the RNA editing to the stability of the RNA structures |
| |
| |
| |
|
Gene summary for TRAF1 |
 Gene summary |
| Gene information | Gene symbol | TRAF1 | Gene ID | 7185 |
| Gene name | TNF receptor associated factor 1 | |
| Synonyms | EBI6|MGC:10353 | |
| Cytomap | 9q33.2 | |
| Type of gene | protein-coding | |
| Description | TNF receptor-associated factor 1Epstein-Bar virus-induced protein 6 | |
| Modification date | 20200327 | |
| UniProtAcc | Q13077, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| TRAF1 | GO:0051092 | positive regulation of NF-kappaB transcription factor activity | 10692572 |
| TRAF1 | GO:2001236 | regulation of extrinsic apoptotic signaling pathway | 10692572 |
Top |
RNA A-to-I events for TRAF1 |
| 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). |
 |
| RNA editing frequencies across three data sets. |
 |
| The number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
 |
| RNA A-to-I editing events in AD. |
| ADediting_1434302(120927399, -), ADediting_1434303(120927404, -), ADediting_1434304(120927431, -), ADediting_1434305(120927454, -), ADediting_1434306(120927476, -), ADediting_1434307(120928173, -), ADediting_1434308(120928181, -), ADediting_1434309(120928200, -), ADediting_1592099(120927400, -), ADediting_1592100(120928141, -), ADediting_1592101(120928157, -), ADediting_1671793(120915726, -), |
Top |
RNA editing positional annotations for TRAF1 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_1434302 | chr9_120927399_- | intronic |
| ADediting_1434303 | chr9_120927404_- | intronic |
| ADediting_1434304 | chr9_120927431_- | intronic |
| ADediting_1434305 | chr9_120927454_- | intronic |
| ADediting_1434306 | chr9_120927476_- | intronic |
| ADediting_1434307 | chr9_120928173_- | intronic |
| ADediting_1434308 | chr9_120928181_- | intronic |
| ADediting_1434309 | chr9_120928200_- | intronic |
| ADediting_1592099 | chr9_120927400_- | intronic |
| ADediting_1592100 | chr9_120928141_- | intronic |
| ADediting_1592101 | chr9_120928157_- | intronic |
| ADediting_1671793 | chr9_120915726_- | intronic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_1434302 | chr9_120927399_- | SINE | MIR | Name=MIRb |
| ADediting_1434303 | chr9_120927404_- | SINE | MIR | Name=MIRb |
| ADediting_1434304 | chr9_120927431_- | SINE | MIR | Name=MIRb |
| ADediting_1434305 | chr9_120927454_- | SINE | MIR | Name=MIRb |
| ADediting_1434306 | chr9_120927476_- | SINE | MIR | Name=MIRb |
| ADediting_1434307 | chr9_120928173_- | SINE | MIR | Name=MIR |
| ADediting_1434308 | chr9_120928181_- | SINE | MIR | Name=MIR |
| ADediting_1434309 | chr9_120928200_- | SINE | MIR | Name=MIR |
| ADediting_1592099 | chr9_120927400_- | SINE | MIR | Name=MIRb |
| ADediting_1592100 | chr9_120928141_- | SINE | MIR | Name=MIR |
| ADediting_1592101 | chr9_120928157_- | SINE | MIR | Name=MIR |
| ADediting_1671793 | chr9_120915726_- | SINE | Alu | Name=AluJr |
Top |
RNA A-to-I editing events in the alternative splicing sites for TRAF1 |
| 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 |
Top |
Differntial gene expression between RNA A-to-I edited versus non-edited samples for TRAF1 |
| 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 |
Top |
Protein coding region RNA A-to-I editings for TRAF1 |
| - Lollipop plot for RNA A-to-I editings across protein structure. * Click on the image to enlarge it in a new window. |
Top |
The effects of the RNA editing to the miRNA binding sites for TRAF1 |
| 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_107020 | chr1_37500952_- | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-5581-3p | chr9 | 120904779 | 120904785 | 7mer-m8 | 120904778 | 120904799 | 140 | -13.21 |
| ADediting_107020 | chr1_37500952_- | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-5581-3p | chr9 | 120904779 | 120904785 | 7mer-m8 | 120904778 | 120904799 | 140 | -13.21 |
| ADediting_107020 | chr1_37500952_- | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-5581-3p | chr9 | 120904779 | 120904785 | 7mer-m8 | 120904778 | 120904799 | 140 | -13.21 |
| ADediting_1535951 | chr14_100874558_+ | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-337-3p | chr9 | 120903463 | 120903469 | 7mer-m8 | 120903462 | 120903483 | 157 | -19.36 |
| ADediting_1535951 | chr14_100874558_+ | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-337-3p | chr9 | 120903463 | 120903469 | 7mer-m8 | 120903462 | 120903483 | 157 | -19.36 |
| ADediting_1535951 | chr14_100874558_+ | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-337-3p | chr9 | 120903463 | 120903469 | 7mer-m8 | 120903462 | 120903483 | 157 | -19.36 |
| ADediting_1596844 | chr1_162342605_+ | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-556-3p | chr9 | 120903707 | 120903713 | 7mer-m8 | 120903706 | 120903726 | 150 | -15.8 |
| ADediting_1596844 | chr1_162342605_+ | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-556-3p | chr9 | 120903707 | 120903713 | 7mer-m8 | 120903706 | 120903726 | 150 | -15.8 |
| ADediting_1596844 | chr1_162342605_+ | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-556-3p | chr9 | 120903707 | 120903713 | 7mer-m8 | 120903706 | 120903726 | 150 | -15.8 |
| ADediting_1631458 | chr19_40282624_- | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-641 | chr9 | 120903072 | 120903079 | 8mer-1a | 120903072 | 120903097 | 150 | -16.9 |
| ADediting_1631458 | chr19_40282624_- | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-641 | chr9 | 120903072 | 120903079 | 8mer-1a | 120903072 | 120903097 | 150 | -16.9 |
| ADediting_1631458 | chr19_40282624_- | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-641 | chr9 | 120903072 | 120903079 | 8mer-1a | 120903072 | 120903097 | 150 | -16.9 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-4512 | chr9 | 120904096 | 120904103 | 8mer-1a | 120904096 | 120904117 | 147 | -18.32 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-4512 | chr9 | 120904096 | 120904103 | 8mer-1a | 120904096 | 120904117 | 147 | -18.32 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-4512 | chr9 | 120904096 | 120904103 | 8mer-1a | 120904096 | 120904117 | 147 | -18.32 |
| ADediting_98288 | chr1_32086990_+ | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-5585-3p | chr9 | 120903047 | 120903053 | 7mer-m8 | 120903046 | 120903065 | 149 | -15.71 |
| ADediting_98288 | chr1_32086990_+ | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-5585-3p | chr9 | 120903047 | 120903053 | 7mer-m8 | 120903046 | 120903065 | 149 | -15.71 |
| ADediting_98288 | chr1_32086990_+ | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-5585-3p | chr9 | 120903047 | 120903053 | 7mer-m8 | 120903046 | 120903065 | 149 | -15.71 |
| 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_- | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-1304-3p | chr9 | 120904753 | 120904759 | 7mer-m8 | 120904752 | 120904771 | 152 | -19.77 |
| ADediting_291761 | chr11_93733708_- | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-1304-3p | chr9 | 120904753 | 120904759 | 7mer-m8 | 120904752 | 120904771 | 152 | -19.77 |
| ADediting_291761 | chr11_93733708_- | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-1304-3p | chr9 | 120904753 | 120904759 | 7mer-m8 | 120904752 | 120904771 | 152 | -19.77 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000373887.8 | TRAF1-201 | hsa-miR-4512 | chr9 | 120903087 | 120903093 | 7mer-m8 | 120903086 | 120903107 | 152 | -25.55 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000540010.1 | TRAF1-202 | hsa-miR-4512 | chr9 | 120903087 | 120903093 | 7mer-m8 | 120903086 | 120903107 | 152 | -25.55 |
| ADediting_496066 | chr15_66496985_- | ENSG00000056558.11 | ENST00000546084.5 | TRAF1-203 | hsa-miR-4512 | chr9 | 120903087 | 120903093 | 7mer-m8 | 120903086 | 120903107 | 152 | -25.55 |
| Differentially expressed gene-miRNA network |
Top |
The effects of the RNA editing to the stability of the RNA structures for TRAF1 |
| - 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 |
Top |
Relation with ADAR for TRAF1 |
| 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.) |
| CER | ADediting_1434302 | chr9_120927399_- | 2.24028372393781e-09 | 0.463935803972968 | 6.06952412379758e-05 | 0.321381821473507 | 0.871670183071251 | 0.013300149544528 |
| CER | ADediting_1434303 | chr9_120927404_- | 4.37471566113998e-10 | 0.481663784685726 | 0.000136659686162878 | 0.306459385208597 | 0.757953388817189 | 0.0253701129328795 |
| 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 | 2.19502830948554e-05 | 0.238522392072095 | 3.18215495155446e-08 | 0.307732978631783 | 3.29269285928826e-11 | 0.365110785744449 |
| AC | 4.58646225992307e-15 | 0.468818557218449 | 4.80774458453793e-06 | 0.284643702813993 | 2.00040928829043e-47 | 0.755373262965722 |
| PCC | 0.016338316543476 | 0.173568226543897 | 0.149854246891425 | 0.104598679291405 | 1.86460806686348e-12 | 0.481074973152794 |
| TCX | 0.378790352212454 | 0.072373232497869 | 3.61130511684874e-05 | -0.330532784466625 | 2.80839784691106e-25 | 0.720273251003088 |
| FP | 1.32058955222716e-09 | 0.434824643556432 | 0.000343225958126789 | 0.265394608636847 | 2.69094562128433e-24 | 0.66729145264584 |
| IFG | 0.454933505392408 | 0.156532029609267 | 0.848791074368883 | -0.0401736612318432 | 0.000730033247655355 | 0.630427256862836 |
| PG | 0.0446044412715603 | 0.147448616884095 | 0.436850483978531 | 0.0573503989111531 | 1.02672365445476e-21 | 0.627018669445835 |
| STG | 0.00597434797201184 | 0.297591595939339 | 0.932979167031718 | -0.00931513406108176 | 3.47420068453719e-07 | 0.522298419465285 |
Top |
Relation with AD stages for TRAF1 |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| TCX | ADediting_1434303 | chr9_120927404_- | 0.00044321742134256 | 0.335249776133022 |
| TCX | ADediting_1434306 | chr9_120927476_- | 7.89013934775317e-05 | 0.373867346582374 |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
| TCX | 0.000950021895494736 | 0.316463005537738 |
Top |
RelatedDrugs for TRAF1 |
| 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 |
Top |
RelatedDiseases for TRAF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| TRAF1 | C0003873 | Rheumatoid Arthritis | 2 | CTD_human |
| TRAF1 | C0000786 | Spontaneous abortion | 1 | CTD_human |
| TRAF1 | C0000822 | Abortion, Tubal | 1 | CTD_human |
| TRAF1 | C0013274 | Patent ductus arteriosus | 1 | CTD_human |
| TRAF1 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| TRAF1 | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
| TRAF1 | C2936170 | Patent Ductus Arteriosus Familial | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|