Dataset: Wang et al. 2024 (male)
This dataset for the male C. elegans contains neurotransmitter expression values from: Wang et al. 2024 with basic anatomical connectivity information from Cook et al. 2019, and monoaminergic receptor expression information from Bentley et al. 2016
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WhiteJSH WhiteN2U White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Yim2024 Yim2024NonNorm Yim2024Contactome Yim2024ContactomeNonNorm Wang2024Herm Wang2024Male OpenWormUnified Test SSData UpdSSData UpdSSData2 GleesonModel OlivaresModel
Dataset taken from Wang et al. 2024. A reader combining neurotransmitter atlas values from Wang et al. 2024 (source: elife-95402-supp2-v1.xlsx; elife-95402-supp3-v1.xlsx) with basic anatomical connectivity information from Cook et al. 2019 Male connectome, and monoaminergic receptor expression information from Bentley et al. 2016. Python Reader: Wang2024MaleReader
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Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 BrainMap A BrainMap B Locomotion 1 Locomotion 2 Locomotion 3 Peptidergic Hubs Nonpharyngeal Neurons (herm) Sensory Neurons (somatic) Motor Neurons (somatic) Motor Neurons (head & sub lat.) Motor Neurons and muscles Interneurons (somatic)
A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019
Cook 2019 Fig 3 (Full1)
A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019
| Connection type | Total size | Values present | Nodes with pre connections | Nodes with post connections |
|---|---|---|---|---|
| Chemical | (17, 17) matrix | 122 non-zero entries 13 nodes with self-connections Avg. weight: 23.590164 Sum of weights: 2878.0 |
HMN, IN1, IN2, IN3, IN4, MNVC, SMN, SN1, SN2, SN3, SN4, SN5, SN6 | HMN, IN1, IN2, IN3, IN4, MNVC, MUBODY, MUHEAD, SMN, SN1, SN2, SN3, SN4, SN5, SN6 |
| Extrasynaptic | (17, 17) matrix | 51 non-zero entries 5 nodes with self-connections Avg. weight: 29.333333 Sum of weights: 1496.0 |
IN1, IN2, SN1, SN3, SN6 | HMN, IN1, IN2, IN3, IN4, MNVC, SMN, SN1, SN2, SN3, SN4, SN5, SN6 |
| Acetylcholine | (17, 17) matrix | 95 non-zero entries 11 nodes with self-connections Avg. weight: 18.284211 Sum of weights: 1737.0 |
HMN, IN1, IN2, IN3, IN4, MNVC, SMN, SN1, SN3, SN4, SN6 | HMN, IN1, IN2, IN3, IN4, MNVC, MUBODY, MUHEAD, SMN, SN1, SN2, SN3, SN4, SN5, SN6 |
| GABA | (17, 17) matrix | 35 non-zero entries 5 nodes with self-connections Avg. weight: 10.600000 Sum of weights: 371.0 |
HMN, IN2, IN3, MNVC, SMN | HMN, IN1, IN2, IN3, IN4, MNVC, MUBODY, MUHEAD, SMN, SN1, SN3, SN4 |
| Glutamate | (17, 17) matrix | 79 non-zero entries 9 nodes with self-connections Avg. weight: 8.835443 Sum of weights: 698.0 |
IN1, IN2, IN3, IN4, SN1, SN2, SN3, SN4, SN5, SN6 | HMN, IN1, IN2, IN3, IN4, MNVC, MUBODY, MUHEAD, SMN, SN1, SN2, SN3, SN4, SN5, SN6 |
| Betaine | (17, 17) matrix | 20 non-zero entries 2 nodes with self-connections Avg. weight: 3.600000 Sum of weights: 72.0 |
IN1, IN3, IN4, SN6 | HMN, IN1, IN2, IN3, IN4, MUHEAD, SMN, SN3, SN4, SN6 |
| Dopamine | (17, 17) matrix | 22 non-zero entries 2 nodes with self-connections Avg. weight: 49.818182 Sum of weights: 1096.0 |
SN1, SN3 | IN1, IN2, IN3, IN4, MNVC, SMN, SN1, SN2, SN3, SN4, SN6 |
| Serotonin | (17, 17) matrix | 9 non-zero entries 1 nodes with self-connections Avg. weight: 14.666667 Sum of weights: 132.0 |
SN6 | HMN, IN1, IN2, IN3, MNVC, SN1, SN3, SN5, SN6 |
| Tyramine | (17, 17) matrix | 12 non-zero entries 1 nodes with self-connections Avg. weight: 17.666667 Sum of weights: 212.0 |
IN1 | HMN, IN1, IN2, IN3, IN4, MNVC, SMN, SN1, SN3, SN4, SN5, SN6 |
| Octopamine | (17, 17) matrix | 8 non-zero entries 1 nodes with self-connections Avg. weight: 7.000000 Sum of weights: 56.0 |
IN2 | IN2, IN3, SMN, SN1, SN2, SN3, SN5, SN6 |
Weight definition: A weight of 1 indicates that the cell expresses the specific neurotransmitter, in addition to an anatomical connection between the pre- and post-synaptic cells (for Glutamate, Acetylcholine, GABA, Betaine), or (for Dopamine, Serotonin, Tyramine, Octopamine) a connection between a monoaminergic receptor-expressing cell and a monoaminergic cell according to Bentley et al. 2016.
Validation tests: See here