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plant_hypocotyl — Plant hypocotyl cellular connectivity (2017)

Description

Networks of the physical contacts between the cells of whole plant hypocotyls (the embryonic stem of seedlings), from Jackson et al. Hypocotyls were imaged with confocal microscopy and segmented into cells in 3D with the MorphoGraphX software, and each cell was annotated with its cell type. Nodes are cells, and an undirected edge connects two cells that are physically adjacent, i.e. share a cell wall, weighted by the area of the shared wall. To account for imaging artifacts, edges between cells sharing less than 2 µm² of wall were removed, except between cells of the vasculature.

There are three biological replicates (_1, _2, _3) for each of eight samples: the Arabidopsis thaliana wild-type ecotypes Columbia (ara_col), Landsberg erecta (ara_ler) and Cape Verde Islands (ara_cvi); the Arabidopsis mutants monopteros (ara_monopteros), cdka1;1 (ara_cdka1) and laterne (ara_laterne); and the species poppy (Papaver rhoeas, poppy) and foxglove (Digitalis purpurea, foxglove).

The networks have the following properties:

  • label: the identifier of the cell in the segmented image.
  • cell_type: the cell type: "trichoblast", "atrichoblast" (the two epidermal cell types), "outer cortex", "inner cortex 2nd layer", "inner cortex 3rd layer" (foxglove only), "endodermis", "vasculature", or "buffer region" (labelled "Buffer region cell" in the source, without further documentation). In poppy_3, the source data give conflicting types for 1,078 cells (the type of a cell is listed separately in each of its edges); the most frequently listed type is used.
  • shared_wall_area (edges): the area of the cell wall shared by the two cells, as computed by MorphoGraphX (in µm²).
Tags
Biological Spatial Weighted Metadata
Citation
  • M. D. B. Jackson, H. Xu, S. Duran-Nebreda, P. Stamm, G. W. Bassel, "Topological analysis of multicellular complexity in the plant hypocotyl." eLife 6, e26023 (2017) 10.7554/eLife.26023 Sci-Hub
Upstream URL OK
https://elifesciences.org/articles/26023
Upstream license
Creative Commons Attribution 4.0 International (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
ara_col_1 2,210 12,188 11.03 3.84 11.90 239.69 0.15 0.37 20 1.00 Undirected Unipartite label cell_type shared_wall_area 71 KiB 118 KiB 122 KiB 95 KiB
ara_col_2 1,940 10,840 11.18 3.73 11.98 200.68 0.18 0.37 19 1.00 Undirected Unipartite label cell_type shared_wall_area 63 KiB 105 KiB 109 KiB 84 KiB
ara_col_3 2,157 12,143 11.26 3.82 12.28 249.58 0.15 0.37 21 1.00 Undirected Unipartite label cell_type shared_wall_area 71 KiB 118 KiB 122 KiB 94 KiB
ara_ler_1 2,411 12,117 10.05 4.45 11.72 221.19 0.07 0.34 21 1.00 Undirected Unipartite label cell_type shared_wall_area 72 KiB 119 KiB 123 KiB 95 KiB
ara_ler_2 2,056 10,844 10.55 4.06 11.75 217.98 0.13 0.36 23 1.00 Undirected Unipartite label cell_type shared_wall_area 65 KiB 111 KiB 112 KiB 86 KiB
ara_ler_3 1,972 10,524 10.67 4.05 11.83 203.77 0.14 0.36 21 1.00 Undirected Unipartite label cell_type shared_wall_area 62 KiB 103 KiB 105 KiB 82 KiB
ara_cvi_1 2,371 13,114 11.06 4.22 12.23 279.96 0.08 0.36 21 1.00 Undirected Unipartite label cell_type shared_wall_area 78 KiB 133 KiB 136 KiB 104 KiB
ara_cvi_2 2,671 14,749 11.04 4.54 13.41 268.24 0.05 0.36 19 1.00 Undirected Unipartite label cell_type shared_wall_area 87 KiB 149 KiB 153 KiB 117 KiB
ara_cvi_3 2,565 14,328 11.17 4.00 12.28 290.96 0.13 0.36 22 1.00 Undirected Unipartite label cell_type shared_wall_area 85 KiB 145 KiB 148 KiB 113 KiB
ara_monopteros_1 749 4,099 10.95 3.95 11.90 106.15 0.12 0.39 15 1.00 Undirected Unipartite label cell_type shared_wall_area 26 KiB 39 KiB 40 KiB 32 KiB
ara_monopteros_2 672 3,590 10.68 3.81 11.71 88.46 0.18 0.39 15 1.00 Undirected Unipartite label cell_type shared_wall_area 23 KiB 36 KiB 36 KiB 29 KiB
ara_monopteros_3 709 3,797 10.71 3.62 11.54 133.29 0.15 0.39 17 1.00 Undirected Unipartite label cell_type shared_wall_area 24 KiB 38 KiB 38 KiB 30 KiB
ara_cdka1_1 1,371 5,956 8.69 5.32 11.88 152.78 0.05 0.31 19 1.00 Undirected Unipartite label cell_type shared_wall_area 38 KiB 61 KiB 62 KiB 48 KiB
ara_cdka1_2 1,796 7,670 8.54 6.25 12.18 145.21 -0.11 0.28 18 1.00 Undirected Unipartite label cell_type shared_wall_area 49 KiB 79 KiB 80 KiB 62 KiB
ara_cdka1_3 1,828 7,694 8.42 5.51 11.76 160.29 -0.01 0.29 18 1.00 Undirected Unipartite label cell_type shared_wall_area 49 KiB 80 KiB 80 KiB 62 KiB
ara_laterne_1 2,712 15,617 11.52 4.25 13.43 244.63 0.08 0.36 20 1.00 Undirected Unipartite label cell_type shared_wall_area 92 KiB 157 KiB 161 KiB 123 KiB
ara_laterne_2 2,308 12,689 11.00 4.57 12.98 135.65 0.06 0.35 17 1.00 Undirected Unipartite label cell_type shared_wall_area 74 KiB 122 KiB 125 KiB 98 KiB
ara_laterne_3 2,846 16,324 11.47 4.44 13.13 261.50 0.07 0.36 20 1.00 Undirected Unipartite label cell_type shared_wall_area 95 KiB 157 KiB 162 KiB 126 KiB
poppy_1 2,507 14,431 11.51 3.89 12.46 181.22 0.12 0.37 18 1.00 Undirected Unipartite label cell_type shared_wall_area 85 KiB 145 KiB 148 KiB 113 KiB
poppy_2 3,777 19,921 10.55 4.61 12.20 295.87 0.06 0.34 22 1.00 Undirected Unipartite label cell_type shared_wall_area 118 KiB 200 KiB 206 KiB 157 KiB
poppy_3 4,417 21,867 9.90 4.73 11.98 384.43 0.06 0.32 22 1.00 Undirected Unipartite label cell_type shared_wall_area 130 KiB 223 KiB 227 KiB 175 KiB
foxglove_1 1,996 11,252 11.27 3.92 12.33 87.88 0.17 0.37 15 1.00 Undirected Unipartite label cell_type shared_wall_area 66 KiB 108 KiB 112 KiB 87 KiB
foxglove_2 3,005 17,043 11.34 4.00 12.35 144.06 0.11 0.37 19 1.00 Undirected Unipartite label cell_type shared_wall_area 101 KiB 171 KiB 176 KiB 134 KiB
foxglove_3 2,916 16,339 11.21 4.38 12.69 181.76 0.06 0.36 18 1.00 Undirected Unipartite label cell_type shared_wall_area 95 KiB 158 KiB 163 KiB 127 KiB