Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages

View ORCID ProfileBradly Alicea, Thomas E. Portegys, Richard Gordon
doi: https://doi.org/10.1101/062539
Bradly Alicea
1Orthogonal Research, Department of Obstetrics & Gynecology, Wayne State University
2OpenWorm Foundation, Department of Obstetrics & Gynecology, Wayne State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bradly Alicea
Thomas E. Portegys
2OpenWorm Foundation, Department of Obstetrics & Gynecology, Wayne State University
3Dialectek LLC, Department of Obstetrics & Gynecology, Wayne State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard Gordon
4Gulf Specimen Marine Laboratory and Aquarium, Department of Obstetrics & Gynecology, Wayne State University
5C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

In this paper, we will introduce a method for calculating and visualizing the information content of embryogenesis called the information isometry technique. We treat cell lineage trees as directed acyclic graphs (DAGs) that can be subject to reordering using various criteria. When we compare alternative orderings of these graphs, they reveal subtle patterns of information. We use one such alternative criteria (e.g. a differentiation code) to sort cells at each level of the tree. Both axial- and differentiation-based orderings can by characterized using a binary classifier to quantify the order of particular cells at each level of a given tree. We calculate a Hamming distance to compare these orderings and reveal differences that result from these ordering criteria. We also introduce a method of visualization through the construction of isometric graphs, or a series of colored points forming isometric lines with each representing a level of the original lineage tree. We show that these graphs reveal biologically significant patterns through comparisons between randomly generated lineage/differentiation trees and the Caenorhabditis elegans lineage/differentiation tree. As a collective indicator of distance between various cell lineage orderings, isometric graphs can reveal a number of emergent patterns within cell lineages and between sublineages, including the relative information content of specific subtrees. These patterns of information content reveal the informative nature of alternative ordering criteria with respect to important trends in development.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted July 07, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages
Bradly Alicea, Thomas E. Portegys, Richard Gordon
bioRxiv 062539; doi: https://doi.org/10.1101/062539
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages
Bradly Alicea, Thomas E. Portegys, Richard Gordon
bioRxiv 062539; doi: https://doi.org/10.1101/062539

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Developmental Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3479)
  • Biochemistry (7318)
  • Bioengineering (5296)
  • Bioinformatics (20197)
  • Biophysics (9976)
  • Cancer Biology (7703)
  • Cell Biology (11250)
  • Clinical Trials (138)
  • Developmental Biology (6418)
  • Ecology (9916)
  • Epidemiology (2065)
  • Evolutionary Biology (13280)
  • Genetics (9352)
  • Genomics (12554)
  • Immunology (7674)
  • Microbiology (18939)
  • Molecular Biology (7417)
  • Neuroscience (40893)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2126)
  • Physiology (3140)
  • Plant Biology (6838)
  • Scientific Communication and Education (1270)
  • Synthetic Biology (1891)
  • Systems Biology (5296)
  • Zoology (1085)