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Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

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Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis https://t.co/ay7We3iT8N
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Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis https://t.co/JpugHx6V7R
RT @Orthogonal_Lab: "Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis", publishe…
231 days ago
"Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis", published today in @PeerJPreprints: https://t.co/YZb3X1b4Ui #Bioinformatics #ComputationalBiology #DevelopmentalBiology
"Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis", published today in @PeerJPreprints: https://t.co/izc1kFfOFq #Bioinformatics #ComputationalBiology #DevelopmentalBiology
Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis https://t.co/icr012OChW
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Supplemental Information

Supplemental File 1: Circular network topologies comparing connections among subtrees and tree levels

The x-axis features a series of circular networks based on the number of above threshold connections between cells at different levels of the tree in a 7 level (128-cell condition) tree.

Rows in descending order: no difference in tree level (0), difference of one level (1), difference of two levels (2), difference of between 3 and 7 levels (3-7).

Columns from left to right: all connections between cells in the AB sublineage only (intra-AB), all connections between cells in the P1 sublineage only (intra-P1), all connections between cells where one cell is from the AB sublineage and the other cell is from the P1 sublineage (inter-AB-P1).

DOI: 10.7287/peerj.preprints.26587v2/supp-1

Supplemental File 2: Heat map of the clique analysis for a 7 level (128-cell condition) tree

Each row represents a unique clique generated from a connectivity matrix of the 7 level tree. The heat map columns represent the number of members in the generated cliques from each octopartite subtree (8 categories). Color coding scheme is presented in the legend to the right of the map.

DOI: 10.7287/peerj.preprints.26587v2/supp-2

Supplemental File 3

Supplemental Table 1: Correlations of positional variance between three pairs of spatial dimensions (X-Y, Y-Z, and X-Z) and within differentiation code categories (4, 6, and 7 level).

DOI: 10.7287/peerj.preprints.26587v2/supp-3

PeerJ peer-reviews (from a previous submission)

Peer-reviews from rejected submission at PeerJ

DOI: 10.7287/peerj.preprints.26587v2/supp-4

Additional Information

Competing Interests

Bradly Alicea is employed by Orthogonal Research and a senior contributor at the OpenWorm Foundation. Richard Gordon is a volunteer by Gulf Specimen Marine Laboratory.

Author Contributions

Bradly J Alicea conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Richard Gordon conceived and designed the experiments, authored or reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

All raw data used in this study are available at Github.

Lineage Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Lineage%20Tree%20DB

Differentiation Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Differentiation%20Tree%20Dataset

All processed data (used in the analyses) are available from the Open Science Framework: https://osf.io/q9jvb/

Funding

The authors received no funding for this work.


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