celegans_extrasynaptic — C. elegans extrasynaptic monoamine and neuropeptide networks (2016)

Description

Directed networks of extrasynaptic ("wireless") signalling between the neurons of the nematode Caenorhabditis elegans (adult hermaphrodite), mediated by monoamines and neuropeptides, from Bentley et al. These networks complement the synaptic and gap-junction connectome, forming a multilayer connectome of the worm.

The networks were inferred from gene expression data, curated from new experiments (GFP reporters for the dopamine receptors dop-5, dop-6 and lgc-53) and from the literature (assisted by the WormBase and WormWeb expression databases). A directed edge goes from a neuron that releases a transmitter (i.e. expresses the transmitter, its biosynthetic enzymes, or transporters) to a neuron that expresses a receptor for it. Edges are not restricted by the physical distance between the neurons.

monoamine: the draft monoamine network, comprising dopamine, serotonin, tyramine and octopamine signalling.
monoamine_dop5_dop6: the same, but including also the putative dopamine receptors dop-5 and dop-6 (a "provisional" dopamine network analysed in the supplementary material of the paper).
neuropeptide: the partial neuropeptide network, including only the peptide-receptor systems with sufficient expression and ligand-receptor interaction data, with interactions limited to biologically plausible peptide-receptor EC50 values (15 neuropeptides matched to 12 receptors).
monoamine_classes, monoamine_classes_dop5_dop6, neuropeptide_classes: the same networks, between neuron classes instead of individual neurons (e.g. the left/right pairs AIAL and AIAR form the class AIA).

Each edge corresponds to one combination of transmitter and receptor, so that a pair of neurons can be connected by several parallel edges (one per receptor expressed by the receiving neuron); self-loops correspond to neurons that express both a transmitter and one of its receptors. In the analyses of the paper, the parallel edges of each monoamine are collapsed into a single edge, and the neuropeptide network is divided into layers by receptor.

The networks have the following properties:

Nodes: name, the name of the neuron (or neuron class).
Edges: transmitter, the monoamine (dopamine, serotonin, tyramine, or octopamine) or neuropeptide (e.g. flp-1, pdf-1) released by the source neuron; receptor, the receptor gene expressed by the target neuron.

Tags

Biological Connectome Unweighted Multigraph Multilayer

Citation

B. Bentley, R. Branicky, C. L. Barnes, Y. L. Chew, E. Yemini, E. T. Bullmore, P. E. Vértes, W. R. Schafer, "The multilayer connectome of Caenorhabditis elegans." PLOS Computational Biology 12(12), e1005283 (2016) 10.1371/journal.pcbi.1005283 Sci-Hub

Upstream URL OK

https://doi.org/10.1371/journal.pcbi.1005283

Upstream license

CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
monoamine	237	2,626	11.08	43.79	40.06	3.63	-0.71	0.19	3	1.00	Directed	Unipartite	name	transmitter receptor	2 KiB	10 KiB	9 KiB	9 KiB
monoamine_dop5_dop6	251	3,162	12.60	53.12	45.15	2.68	-0.72	0.17	3	1.00	Directed	Unipartite	name	transmitter receptor	2 KiB	11 KiB	11 KiB	11 KiB
neuropeptide	239	8,931	37.37	68.33	80.54	2.42	-0.03	0.59	3	1.00	Directed	Unipartite	name	transmitter receptor	3 KiB	29 KiB	29 KiB	27 KiB
monoamine_classes	86	348	4.05	13.76	13.97	3.66	-0.73	0.21	3	1.00	Directed	Unipartite	name	transmitter receptor	2 KiB	3 KiB	2 KiB	3 KiB
monoamine_classes_dop5_dop6	93	444	4.77	17.55	16.34	2.76	-0.71	0.19	3	1.00	Directed	Unipartite	name	transmitter receptor	2 KiB	3 KiB	3 KiB	3 KiB
neuropeptide_classes	97	1,973	20.34	31.54	37.18	2.43	0.03	0.60	3	1.00	Directed	Unipartite	name	transmitter receptor	2 KiB	8 KiB	7 KiB	7 KiB