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Related Experiment Video

Updated: Apr 19, 2026

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Published on: November 1, 2014

Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

Carol A Soderlund¹, William M Nelson¹, Stephen A Goff²

¹BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America.

|December 27, 2014

Summary

Allele Workbench software analyzes allele-specific expression in hybrid organisms, aiding heterosis research by evaluating allelic imbalance and its impact on protein folding. This tool facilitates deeper understanding of gene expression in hybrids.

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Last Updated: Apr 19, 2026

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

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Published on: November 1, 2014

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

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Published on: March 5, 2022

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Transcriptome sequencing reveals gene expression patterns, crucial for understanding traits like heterosis (hybrid vigor).
Allele-specific expression (ASE) analysis compares gene expression between parental alleles in hybrids, offering insights into hybrid performance.
Previous studies on heterosis have utilized differential and allele-specific expression analyses.

Purpose of the Study:

To introduce Allele Workbench, a software package designed for analyzing allele-specific expression in the context of heterosis research.
To provide a comprehensive pipeline and user-friendly Java interfaces for database construction, querying, and visualization of ASE data.
To enable the assessment of allelic imbalance at SNP and transcript levels and its potential impact on protein folding.

Main Methods:

Development of a distributable software package including a pipeline and Java interfaces for database management and results querying.
Inputting reference genome, annotation file, and RNA-Seq libraries (with replicates) to evaluate allelic imbalance.
Annotating variants for their effect on protein folding and exporting parental protein sequences for further analysis.

Main Results:

The software evaluates allelic imbalance at both SNP and transcript levels.
It identifies transcripts exhibiting significant, opposing directional allele-specific expression.
Results can be integrated with the Transcriptome Computational Workbench for gene ontology term analysis.

Conclusions:

Allele Workbench provides a robust platform for detailed allele-specific expression analysis in hybrid systems.
The software aids in understanding the genetic basis of heterosis by dissecting parental allele contributions to gene expression.
Integration with other computational tools extends its utility for comprehensive transcriptome analysis and functional annotation.