Dataset: Yim et al. 2024 Contactome
Reconstruction of the contactome of the dauer, a distinct developmental stage of C. elegans, contains a symmetric matrix measuring physical contact between pre/post cells. Every cell in the reconstructed EM volume was traced voxel by voxel; these labelled cells were then expanded until the extracellular gaps between them closed, and the area of each resulting point of contact summed. This connectome dataset contains normalized contact areas/weights to ease comparison to other datasets.
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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 Yim et al. 2024. Data extracted from 41467_2024_45943_MOESM9_ESM.xlsx, Yim et al. 2024 Dauer connectome (Contactome; Normalized). Python Reader: Yim2024ContactomeDataReader
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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 and muscles - Interneurons (somatic) -
All hermaphrodite sensory neurons except those in the pharynx
Sensory Neurons (somatic) (SensorySomaticH)
All hermaphrodite sensory neurons except those in the pharynx
| Connection type | Total size | Values present | Nodes with pre connections | Nodes with post connections |
|---|---|---|---|---|
| Contact | (83, 83) matrix | 1024 non-zero entries Matrix is symmetric with 512 unique pairs (total unique pair weight: 554.6647126673195) Avg. weight: 1.083330 Sum of weights: 1109.329425334639 |
ADEL, ADER, ADFL, ADFR, ADLL, ADLR, AFDL, AFDR, ALML, ALMR, ALNL, ALNR, AQR, ASEL, ASER, ASGL, ASGR, ASHL, ASHR, ASIL, ASIR, ASJL, ASJR, ASKL, ASKR, AVM, AWAL, AWAR, AWBL, AWBR, AWCL, AWCR, BAGL, BAGR, CEPDL, CEPDR, CEPVL, CEPVR, DVA, FLPL, FLPR, IL1DL, IL1DR, IL1L, IL1R, IL1VL, IL1VR, IL2DL, IL2DR, IL2L, IL2R, IL2VL, IL2VR, OLLL, OLLR, OLQDL, OLQDR, OLQVL, OLQVR, PLNL, PLNR, SDQL, SDQR, URXL, URXR, URYDL, URYDR, URYVL, URYVR | ADEL, ADER, ADFL, ADFR, ADLL, ADLR, AFDL, AFDR, ALML, ALMR, ALNL, ALNR, AQR, ASEL, ASER, ASGL, ASGR, ASHL, ASHR, ASIL, ASIR, ASJL, ASJR, ASKL, ASKR, AVM, AWAL, AWAR, AWBL, AWBR, AWCL, AWCR, BAGL, BAGR, CEPDL, CEPDR, CEPVL, CEPVR, DVA, FLPL, FLPR, IL1DL, IL1DR, IL1L, IL1R, IL1VL, IL1VR, IL2DL, IL2DR, IL2L, IL2R, IL2VL, IL2VR, OLLL, OLLR, OLQDL, OLQDR, OLQVL, OLQVR, PLNL, PLNR, SDQL, SDQR, URXL, URXR, URYDL, URYDR, URYVL, URYVR |
| Nodes in current view (83 total) xxxxxxxxxxxxxxxxxxxxxxxxx |
Num cells in node (83 total) |
Num in this dataset (69 total) |
Cells in node |
|---|---|---|---|
| ADEL | 1 | 1 | ADEL |
| ADER | 1 | 1 | ADER |
| ADFL | 1 | 1 | ADFL |
| ADFR | 1 | 1 | ADFR |
| ADLL | 1 | 1 | ADLL |
| ADLR | 1 | 1 | ADLR |
| AFDL | 1 | 1 | AFDL |
| AFDR | 1 | 1 | AFDR |
| ALML | 1 | 1 | ALML |
| ALMR | 1 | 1 | ALMR |
| ALNL | 1 | 1 | ALNL |
| ALNR | 1 | 1 | ALNR |
| AQR | 1 | 1 | AQR |
| ASEL | 1 | 1 | ASEL |
| ASER | 1 | 1 | ASER |
| ASGL | 1 | 1 | ASGL |
| ASGR | 1 | 1 | ASGR |
| ASHL | 1 | 1 | ASHL |
| ASHR | 1 | 1 | ASHR |
| ASIL | 1 | 1 | ASIL |
| ASIR | 1 | 1 | ASIR |
| ASJL | 1 | 1 | ASJL |
| ASJR | 1 | 1 | ASJR |
| ASKL | 1 | 1 | ASKL |
| ASKR | 1 | 1 | ASKR |
| AVM | 1 | 1 | AVM |
| AWAL | 1 | 1 | AWAL |
| AWAR | 1 | 1 | AWAR |
| AWBL | 1 | 1 | AWBL |
| AWBR | 1 | 1 | AWBR |
| AWCL | 1 | 1 | AWCL |
| AWCR | 1 | 1 | AWCR |
| BAGL | 1 | 1 | BAGL |
| BAGR | 1 | 1 | BAGR |
| CEPDL | 1 | 1 | CEPDL |
| CEPDR | 1 | 1 | CEPDR |
| CEPVL | 1 | 1 | CEPVL |
| CEPVR | 1 | 1 | CEPVR |
| DVA | 1 | 1 | DVA |
| FLPL | 1 | 1 | FLPL |
| FLPR | 1 | 1 | FLPR |
| IL1DL | 1 | 1 | IL1DL |
| IL1DR | 1 | 1 | IL1DR |
| IL1L | 1 | 1 | IL1L |
| IL1R | 1 | 1 | IL1R |
| IL1VL | 1 | 1 | IL1VL |
| IL1VR | 1 | 1 | IL1VR |
| IL2DL | 1 | 1 | IL2DL |
| IL2DR | 1 | 1 | IL2DR |
| IL2L | 1 | 1 | IL2L |
| IL2R | 1 | 1 | IL2R |
| IL2VL | 1 | 1 | IL2VL |
| IL2VR | 1 | 1 | IL2VR |
| OLLL | 1 | 1 | OLLL |
| OLLR | 1 | 1 | OLLR |
| OLQDL | 1 | 1 | OLQDL |
| OLQDR | 1 | 1 | OLQDR |
| OLQVL | 1 | 1 | OLQVL |
| OLQVR | 1 | 1 | OLQVR |
| PDEL | 1 | 0 | PDEL |
| PDER | 1 | 0 | PDER |
| PHAL | 1 | 0 | PHAL |
| PHAR | 1 | 0 | PHAR |
| PHBL | 1 | 0 | PHBL |
| PHBR | 1 | 0 | PHBR |
| PHCL | 1 | 0 | PHCL |
| PHCR | 1 | 0 | PHCR |
| PLML | 1 | 0 | PLML |
| PLMR | 1 | 0 | PLMR |
| PLNL | 1 | 1 | PLNL |
| PLNR | 1 | 1 | PLNR |
| PQR | 1 | 0 | PQR |
| PVDL | 1 | 0 | PVDL |
| PVDR | 1 | 0 | PVDR |
| PVM | 1 | 0 | PVM |
| SDQL | 1 | 1 | SDQL |
| SDQR | 1 | 1 | SDQR |
| URXL | 1 | 1 | URXL |
| URXR | 1 | 1 | URXR |
| URYDL | 1 | 1 | URYDL |
| URYDR | 1 | 1 | URYDR |
| URYVL | 1 | 1 | URYVL |
| URYVR | 1 | 1 | URYVR |
Weight definition: Weights are the total contact area (nm2) between a pair of cells. In this dataset, these are normalized by the standard deviation of connection weights without the top 5th percentile to remove the bias due to the big outliers
Validation tests: See here