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Protocols

REDIportal specifications

Information


Unique identifier OMICS_17524
Name REDIportal
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Ernesto Picardi

Publication for REDIportal

REDIportal citations

 (5)
library_books

Whole transcriptome profiling of Late Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease

2018
Sci Rep
PMCID: 5844946
PMID: 29523845
DOI: 10.1038/s41598-018-22701-2

[…] d using custom scripts and according to the methodology described in Bazak et al.. RNA editing levels in recoding sites were assessed using REDItools and providing a list of 1585 known positions from REDIportal database in which RNA editing causes amino acid change. Only positions supported by RNAseq reads in at least three samples per group and showing a median editing level higher than 0.1 were […]

call_split

A survey on cellular RNA editing activity in response to Candida albicans infections

2018
BMC Genomics
PMCID: 5780849
PMID: 29363428
DOI: 10.1186/s12864-017-4374-2
call_split See protocol

[…] R package Venn Diagram [] was used to calculate and draw the overlapping between our identified RNA editing sites and those included in the databases: DARNED, RADAR and REDIportal. R package ggplot2 [] was used for plotting other figures. For statistics testing with distribution of A-to-I RNA editing data, the nonparametric test, Kruskal-Wallis rank sum test, was per […]

library_books

Global analysis of A to I RNA editing reveals association with common disease variants

2018
PeerJ
PMCID: 5844249
PMID: 29527417
DOI: 10.7717/peerj.4466

[…] ted, conserved editing sites had higher editing ratios (medianconserved = 0.30, mediannotconserved = 0.05, P < 2.2e−16, Mann–Whitney U test). Moreover, 80% (52/65) of these sites had been reported in REDIportal (), and 35% (23/65) had been reported in the literature (). The classical example of recoding in GRIA2 (glutamate ionotropic receptor AMPA type subunit 2) was found at the known site (chr4: […]

call_split

An Evolutionary Landscape of A to I RNA Editome across Metazoan Species

2017
Genome Biol Evol
PMCID: 5800060
PMID: 29294013
DOI: 10.1093/gbe/evx277
call_split See protocol

[…] n (releases 66 and 85) is given in , online. Compared with previously identified A-to-I editing sites in human, mouse, and fly [collected in the well-known public databases: DARNED (), RADAR (), and REDIportal ()], we found that most the identified human editing sites (∼90%) were also detected in the public databases (, online). In contrast, more than one third of the identified mouse and fly A- […]

call_split

RNA editing signature during myeloid leukemia cell differentiation

2017
Leukemia
PMCID: 5729351
PMID: 28484266
DOI: 10.1038/leu.2017.134
call_split See protocol

[…] was calculated using custom scripts according to the methodology described in Bazak et al. RNA editing in recoding sites was assessed using REDItools and providing a list of 2955 known positions from REDIportal database in which RNA editing causes amino-acid change. This initial list was filtered in order to include only RNA editing positions supported by RNA-seq reads in all replicates. In additi […]

Citations

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REDIportal funding source(s)
Italian Ministero dell’Istruzione, Universita e Ricerca (MIUR) [PRIN 2012]; Consiglio Nazionale delle Ricerche: Flagship Project Epigen, Medicina Personalizzata, Aging Program, Interomics and Elixir-ITA.

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