• Overview
• Submit
  • Input File
  • Data Uploading
  • Job Status Checking
  • Result Availability
  • Example Result

Overview

MIRIA is a user-ferendly webserver that integrates statistics and visualization techniques, to facilitate comprehensive analysis of RNA editing sites data identified by other pipelines and software. The MIRIA provides several analysis functions, including RNA editing types statistic, genomic feature annotation, editing level statistic, editing sites distribution, tissue-specific analysis and conservation analysis.

Submit

Input File

MIRIA required user to upload a compressed file (.zip format) containing all RNA editing files of different mammals. The architecture of the zip file has two layers. The first layer contains all species folders (e.g., human, mouse, rat) and the second layer, inside each species folder, contains all RNA editing files of this species (e.g., tissue1.res, tissue2.res, tissue3.res) (Figure 1). The format of the single RNA editing file (.res) is listed below (Table 1).

Figure 1. The example input file of MIRIA

Table 1. The format of a single RNA editing file. Chromosome: Name of chromosome. Location (0/1 base): Position of the editing site in the chromosome. Type: Type of the identified editing site (e.g. AG means ’A-to-G’, etc.). Supporting information: Number of supporting reads for this editing site. Strand: Possible values are: ’.’, ’+’, and ’-’ which correspond to ’uncertain’, ’positive strand’, and ’negative strand’ respectively. AD:DP: Number of reads that has this editing site and the number of reads that cover this location. This file is the output file of RNA editing sites identification tool, SPRINT. Users need to convert other RNA editing sites file format to this format before uploading input file.

Data Uploading

Users can analyze their data by uploading their .zip input file in MIRIA analysis page (clicking ANALYSIS link in navigation bar)(Figure 2).

Figure 2. Analaysis page of MIRIA

Paramaters

• Reference Type: the prefix of chromosome id: with or without chr
• Minimum Reads Coverage for Each Editing Site: the minimum supporting reads number to filter out false positive editing sites. Default value is 1.
• Minimum Reads Coverage for Each Editing Site: the minimum reads coverage to filter out false positive editing sites.Default value is 1.
• Strand: strand information of input data. For strand-specific data, 'AG +' and 'TC -' are all thought to be A-to-G (A-to-I editing). For non-strand-specific data, there are two ways to estimate the A-to-G rate: 'AG +/-' and 'TC +/-' are all thought to be A-to-G (A-to-I editing).
• Entropy Cutoff: the Entropy cuffoff for tissue specific rna editing sites. The value should be in range 0 to 1. The default value is 0.4.
• Conservation Site Number Cutoff: this value will be used to select top # of all conservered sites to draw clustering heatmap, sorted by average editing level with decreasing order. The value should be less than 400. The default value is 200 (if exceeds).

Job Status Checking

After analysis job submission, a job id will be assigned (Figure 3) and users can check their job status using this job id by clicking check you job status link in analysis page (Figure 4).

Figure 3: Assigned job id after analaysis job submission

Figure 4: Check job status link in analysis page

Result Availability

After the job completion, users can view the result by clicking “view result” link on check job status page (Figure 5).

Figure 5. View result link in check job status page

Example Result

The example result page can be accessed by clicking Example Result link in navigation bar.