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INFO GRAB: An interactive shiny application for gene expression analysis and visualization.

Oliver Brown1, Andressa Oliveira de Lima1, Yvonne Drechsler2

  • 1Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA 98195, USA.

Genomics
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Summary
This summary is machine-generated.

INFO GRAB is a new tool for exploring chicken gene expression data. This application helps researchers analyze transcriptomic data to understand genetic traits and regulatory mechanisms in poultry.

Keywords:
Allele-specific expressionFunctional annotation of animal genomes (FAANG)Genome annotationTissue-specific expressionTranscriptome

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Area of Science:

  • Genomics
  • Bioinformatics
  • Transcriptomics

Background:

  • Gene expression analysis is crucial for understanding biological processes.
  • Poultry genomics research requires efficient tools for large-scale transcriptomic data analysis.
  • Existing tools may lack integrated functionalities for diverse analyses like differential, tissue-specific, and allele-specific expression.

Purpose of the Study:

  • To develop an interactive Shiny application, INFO GRAB, for comprehensive gene expression data exploration in chicken.
  • To integrate multiple analysis functionalities including differential expression, tissue-specific expression, and allele-specific expression.
  • To provide advanced visualization tools and an embedded genome viewer for enhanced data interpretation.

Main Methods:

  • Development of an interactive Shiny application.
  • Integration of DESeq2 for differential expression analysis.
  • Utilization of Tau-based metrics for expression analysis.
  • Incorporation of curated multi-omic data.
  • Implementation of advanced plotting features (volcano plots, heatmaps, PCA, correlation) and a genome viewer.

Main Results:

  • INFO GRAB provides a user-friendly interface for exploring chicken gene expression data.
  • The application integrates differential, tissue-specific, and allele-specific expression analyses.
  • Advanced visualization tools facilitate the interpretation of complex transcriptomic data.
  • The tool supports large-scale transcriptomic analyses, aiding in the investigation of regulatory mechanisms and genetic traits.

Conclusions:

  • INFO GRAB offers a powerful and streamlined platform for poultry genomics research.
  • The application empowers researchers to efficiently analyze and visualize gene expression data.
  • INFO GRAB advances the study of regulatory mechanisms and complex genetic traits in chickens.