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Tissue enrichment analysis for C. elegans genomics.

David Angeles-Albores1, Raymond Y N Lee1, Juancarlos Chan1

  • 1HHMI and California Institute of Technology, Division of Biology and Biological Engineering, 1200 E California Blvd, Pasadena, 91125, USA.

BMC Bioinformatics
|September 14, 2016
PubMed
Summary
This summary is machine-generated.

We developed Tissue Enrichment Analysis (TEA) to identify specific C. elegans tissues in gene expression datasets. This tool aids hypothesis generation by analyzing gene sets and visualizing tissue enrichment, even at the single-cell level.

Keywords:
Anatomy ontologyGene ontologyHigh-throughput biologyRNA-seqWormBase

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Area of Science:

  • Genomics
  • Bioinformatics
  • Developmental Biology

Background:

  • Gene expression analysis methods have advanced rapidly, generating large datasets that are challenging to interpret.
  • Gene Ontology (GO) aids analysis but lacks anatomical detail for Caenorhabditis elegans.
  • Ontology enrichment analysis helps form hypotheses but can be verbose.

Purpose of the Study:

  • To develop a tool for identifying enrichment of C. elegans tissues within gene sets.
  • To create a user-friendly website GUI for accessing the analysis tool.
  • To address the verbosity of ontology enrichment by developing a filtering algorithm.

Main Methods:

  • Developed a tool for C. elegans tissue enrichment analysis.
  • Created a website GUI for tool accessibility.
  • Implemented a filtering algorithm to reduce ontology size.
  • Validated the tool with 30 gold standards from WormBase Expression Cluster data.

Main Results:

  • The tool successfully identifies enrichment of C. elegans tissues in gene sets.
  • The filtering algorithm reduced ontology size by an order of magnitude.
  • The tool can discriminate between embryonic and larval tissues, and identify tissues at the single-cell level.
  • Identified down-regulated neuronal tissues in C. elegans due to pathogen infection.

Conclusions:

  • Tissue Enrichment Analysis (TEA) is available in WormBase and via pip installer.
  • TEA analyzes a slimmed-down C. elegans tissue ontology for term enrichment.
  • Provides users with text and graphical representations of enrichment results.