In GranderLab/miR34a_asRNA_project: The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.

packages <- c(
    "tidyverse",
    "printr",
    "ggthemes",
    "readr",
    "miR34AasRNAproject",
    "grid",
    "gtable"
)
purrr::walk(packages, library, character.only = TRUE)
rm(packages)

Introduction

We utilized a bioinformatic approach to evaluate the coding potential of the miR34a asRNA transcript. The Coding-potential assessment tool uses a linear regression model to evaluate coding-potential by examining ORF length, ORF coverage, Fickett score and hexamer score. We further confirmed these results using the Coding-potential Calculator which utilizes a support based machine-based classifier and accesses an alternate set of discriminatory features.

Methods

Protein-coding capacity was evaluated using the Coding-potential Assessment Tool and Coding-potential Calculator with default settings. Transcript sequences for use with Coding-potential Assessment Tool were downloaded from the UCSC genome browser using the following IDs: HOTAIR (ENST00000455246.1), XIST (ENST00000429829.1), β-actin (ENST00000331789.5), Tubulin (ENST00000427480.1), and MYC (ENST00000377970). Transcript sequences for use with Coding-potential Calculator were downloaded from the UCSC genome browser using the following IDs: HOTAIR (uc031qho.1), β-actin (uc003soq.4).

Results

Coding Potential Assesment Tool

cpat <- getData("Figure 1f")
cpat

Coding potential analysis results from the Coding-potential Assessment Tool including miR34a asRNA and two characterized non-coding transcripts (HOTAIR and XIST) and 3 known coding transcripts (β-actin, tubulin, and MYC).

*Results for Coding-potential Calculator are located in Supplementary Figure 2e.

Conclusions

Results indicated that miR34a asRNA has a similar lack of coding capacity to the known non-coding transcripts HOTAIR and XIST and differs greatly when examining these parameters to the known coding transcripts beta-actin, tubulin, and MYC. However, to fully evaluate coding potential methods such as mass spectrometry or ribosome profiling must be used.

sessionInfo()

GranderLab/miR34a_asRNA_project documentation built on May 26, 2019, 7:26 a.m.