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Depletion of Specific Cell Populations by Complement Depletion
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A new sequence logo plot to highlight enrichment and depletion.

Kushal K Dey1, Dongyue Xie2, Matthew Stephens2,3

  • 1Department of Statistics, University of Chicago, Chicago, 60637, USA. kkdey@uchicago.edu.

BMC Bioinformatics
|December 12, 2018
PubMed
Summary

We introduce EDLogo plots to visualize sequence data, highlighting both enrichment and depletion effectively. Our R package, Logolas, offers customizable visualizations and improved pattern detection for diverse biological sequence analyses.

Keywords:
EDLogoEnrichment depletionLogo plotsString symbols

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Area of Science:

  • Bioinformatics and Computational Biology
  • Genomics and Proteomics
  • Data Visualization

Background:

  • Sequence logo plots are standard for visualizing sequence motifs in DNA, RNA, and proteins.
  • Traditional logos primarily show symbol enrichment, often missing significant depletions.
  • Existing methods for depicting depletion can lead to visually cluttered plots.

Purpose of the Study:

  • To develop a novel sequence logo plot, EDLogo, that visualizes both enrichment and depletion.
  • To create a user-friendly and customizable R package, Logolas, for generating various logo plots.
  • To enhance the visualization of sequence patterns by incorporating Empirical Bayes methods.

Main Methods:

  • Introduction of the EDLogo plot for simultaneous visualization of enrichment and depletion.
  • Development of the R package Logolas, offering high customizability and extended element types (strings).
  • Implementation of Empirical Bayes methods to stabilize estimates and improve pattern significance.

Main Results:

  • EDLogo plots effectively highlight both enrichment and depletion with minimal visual clutter.
  • The Logolas package enables the creation of diverse logo plots, including EDLogos.
  • Applications demonstrated on transcription factor binding sites, protein alignments, and cancer mutation profiles.

Conclusions:

  • EDLogo plots provide a powerful tool for visualizing sequence character enrichment and depletion.
  • The Logolas software facilitates flexible and effective data analysis across various biological sequence applications.
  • This approach aids data analysts in identifying significant patterns in sequence data.