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Flow-Based Network Analysis of the Caenorhabditis elegans Connectome

Bacik, Karol A. and Schaub, Michael T. and Beguerisse-Díaz, Mariano and Billeh, Yazan N. and Barahona, Mauricio (2016) Flow-Based Network Analysis of the Caenorhabditis elegans Connectome. PLOS Computational Biology, 12 (8). Art. No. e1005055. ISSN 1553-7358. PMCID PMC4975510. https://resolver.caltech.edu/CaltechAUTHORS:20160815-141402908

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[img] MS Excel (S1 Data. Supplementary Data as XLS spreadsheet) - Supplemental Material
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[img] PDF (S1 Text. Comparison of MS partitions to other methods) - Supplemental Material
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[img] PDF (S2 Text. Comparison of RBS flow roles with other analyses of roles) - Supplemental Material
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[img] Image (TIFF) (S1 Fig. Full analysis of the C. elegans connectome with Markov Stability (MS)) - Supplemental Material
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[img] Image (TIFF) (S2 Fig. The asymmetry in the normalised conditional entropy of the optimised MS partitions signals a quasi-hierarchical community structure) - Supplemental Material
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[img] Image (TIFF) (S3 Fig. The effect of ablations and other network measures) - Supplemental Material
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[img] Image (TIFF) (S4 Fig. Finding role profiles with RBS) - Supplemental Material
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[img] Image (TIFF) (S5 Fig. Distribution of RBS flow roles across MS communities) - Supplemental Material
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[img] Image (TIFF) (S6 Fig. Comparison of RBS flow roles to roles obtained using Regular Equivalence) - Supplemental Material
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[img] Image (TIFF) (S7 Fig. Summary of the procedure for signal propagation analysis of posterior mechanosensory stimulus scenario (i1)) - Supplemental Material
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[img] Image (TIFF) (S8 Fig. Signal propagation of the anterior mechanosensory stimulus (i2)) - Supplemental Material
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[img] Image (TIFF) (S9 Fig. Signal propagation: posterior chemosensory stimulus (i3)) - Supplemental Material
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[img] Image (TIFF) (S10 Fig. Signal propagation: anterior chemosensory stimulus (i4)) - Supplemental Material
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[img] Image (TIFF) (S11 Fig. Peak times of strong response neurons by RBS roles for each of the four input scenarios (i1)-(i4)) - Supplemental Material
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[img] Image (TIFF) (S12 Fig. Peak overshoots against other network measures) - Supplemental Material
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Abstract

We exploit flow propagation on the directed neuronal network of the nematode C. elegans to reveal dynamically relevant features of its connectome. We find flow-based groupings of neurons at different levels of granularity, which we relate to functional and anatomical constituents of its nervous system. A systematic in silico evaluation of the full set of single and double neuron ablations is used to identify deletions that induce the most severe disruptions of the multi-resolution flow structure. Such ablations are linked to functionally relevant neurons, and suggest potential candidates for further in vivo investigation. In addition, we use the directional patterns of incoming and outgoing network flows at all scales to identify flow profiles for the neurons in the connectome, without pre-imposing a priori categories. The four flow roles identified are linked to signal propagation motivated by biological input-response scenarios.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pcbi.1005055DOIArticle
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005055PublisherArticle
http://dx.doi.org/10.1371/journal.pcbi.1005055.s001DOIS1 Data
http://dx.doi.org/10.1371/journal.pcbi.1005055.s002DOIS1 Text
http://dx.doi.org/10.1371/journal.pcbi.1005055.s003DOIS2 Text
http://dx.doi.org/10.1371/journal.pcbi.1005055.s004DOIS1 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s005DOIS2 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s006DOIS3 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s007DOIS4 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s008DOIS5 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s009DOIS6 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s010DOIS7 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s011DOIS8 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s012DOIS9 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s013DOIS10 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s014DOIS11 Fig.
http://dx.doi.org/10.1371/journal.pcbi.1005055.s015DOIS12 Fig.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4975510/PubMed CentralArticle
ORCID:
AuthorORCID
Schaub, Michael T.0000-0003-2426-6404
Billeh, Yazan N.0000-0001-5200-4992
Additional Information:© 2016 Bacik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: January 12, 2016; Accepted: July 12, 2016; Published: August 5, 2016. Data Availability: All relevant data are within the paper and its Supporting Information files. Funding: KAB acknowledges an Award from the Imperial College Undergraduate Research Opportunities Programme (UROP). MTS acknowledges support from the ARC and the Belgium network DYSCO (Dynamical Systems, Control and Optimisation). YNB acknowledges support from the G. Harold and Leila Y. Mathers Foundation. MBD acknowledges support from the James S. McDonnell Foundation Postdoctoral Program in Complexity Science/Complex Systems Fellowship Award (220020349-CS/PD Fellow). MB acknowledges support from EPSRC grants EP/I017267/1 and EP/N014529/1. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist. Author Contributions: Conceived and designed the experiments: KAB MTS MBD MB. Performed the experiments: KB MTS MBD. Analyzed the data: KAB MTS MBD YNB MB. Wrote the paper: KAB MTS MBD YNB MB. Created the figures: KAB MTS MBD MB.
Funders:
Funding AgencyGrant Number
Imperial CollegeUNSPECIFIED
Australian Research CouncilUNSPECIFIED
Belgium Network DYSCOUNSPECIFIED
G. Harold and Leila Y. Mathers Charitable FoundationUNSPECIFIED
James S. McDonnell Foundation220020349-CS
Engineering and Physical Sciences Research Council (EPSRC)EP/I017267/1
Engineering and Physical Sciences Research Council (EPSRC)EP/N014529/1
Issue or Number:8
PubMed Central ID:PMC4975510
Record Number:CaltechAUTHORS:20160815-141402908
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160815-141402908
Official Citation:Bacik KA, Schaub MT, Beguerisse-Díaz M, Billeh YN, Barahona M (2016) Flow-Based Network Analysis of the Caenorhabditis elegans Connectome. PLoS Comput Biol 12(8): e1005055. doi:10.1371/journal.pcbi.1005055
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:69631
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Aug 2016 21:48
Last Modified:03 Oct 2019 10:24

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