Table S5: Increase in connectivity due to the utilisation of the TOM. The last column shows the ratio of sums of all pairwise connectivities between two sets of genes. The numerator is calculated with TOM, and the denominator without the TOM, for the same two sets of genes. We performed this calculation for all genes, and then for various gene sets derived from examining the WGCNA gene clusters. Gene sets are named by the WGCNA modules from which they are selected by retaining the overlapping genes between a TOM module and a "no TOM" module. When the two sets of genes indicated are the same, we took the sums of the lower triangular sub-matrix from the connectivity matrices. Ratio of sums of First set of genes Second set of genes connectivities All All 2.410 Genes that were in one of our key modules with TOM, but in the catchall grey cluster without the TOM TOM:Navy noTOM:Grey TOM:Navy noTOM:Grey 1.485 – – TOM:Orange noTOM:Grey TOM:Orange noTOM:Grey 2.034 – – TOM:Orchid noTOM:Grey TOM:Orchid noTOM:Grey 2.099 – – TOM:Plum noTOM:Grey TOM:Plum noTOM:Grey 2.037 – – Same first set as above; while the second set are the genes in one of our key clusters. TOM:Navy noTOM:Grey TOM:Navy noTOM:Red 2.875 – – TOM:Orange noTOM:Grey TOM:Orange noTOM:Green 4.843 – – TOM:Orchid noTOM:Grey TOM:Orchid noTOM:Brown 4.374 – – TOM:Plum noTOM:Grey TOM:Plum noTOM:Pink 6.487 – – Genes with similar clustering with and without TOM TOM:Navy noTOM:Red TOM:Navy noTOM:Red 1.424 – – TOM:Orange noTOM:Green TOM:Orange noTOM:Green 1.671 – – TOM:Orchid noTOM:Brown TOM:Orchid noTOM:Brown 1.685 – – TOM:Plum noTOM:Pink TOM:Plum noTOM:Pink 1.206 – – Table S6. Complete set of notation Notation Description
Table S5: Increase in connectivity due to the utilisation of the TOM. The last column shows the ratio of sums of all pairwise connectivities between two sets of genes. The numerator is calculated with TOM, and the denominator without the TOM, for the same two sets of genes. We performed this calculation for all genes, and then for various gene sets derived from examining the WGCNA gene clusters. Gene sets are named by the WGCNA modules from which they are selected by retaining the overlapping genes between a TOM module and a "no TOM" module. When the two sets of genes indicated are the same, we took the sums of the lower triangular sub-matrix from the connectivity matrices. First set of genes Second set of genes Ratio of sums of connectivities All All 2.410 Genes that were in one of our key modules with TOM, but in the catchall grey cluster without the TOM TOM:Navy – noTOM:Grey TOM:Navy – noTOM:Grey 1.485 TOM:Orange – noTOM:Grey TOM:Orange – noTOM:Grey 2.034 TOM:Orchid – noTOM:Grey TOM:Orchid – noTOM:Grey 2.099 TOM:Plum – noTOM:Grey TOM:Plum – noTOM:Grey 2.037 Same first set as above; while the second set are the genes in one of our key clusters. TOM:Navy – noTOM:Grey TOM:Navy – noTOM:Red 2.875 TOM:Orange – noTOM:Grey TOM:Orange – noTOM:Green 4.843 TOM:Orchid – noTOM:Grey TOM:Orchid – noTOM:Brown 4.374 TOM:Plum – noTOM:Grey TOM:Plum – noTOM:Pink 6.487 Genes with similar clustering with and without TOM TOM:Navy – noTOM:Red TOM:Navy – noTOM:Red 1.424 TOM:Orange – noTOM:Green TOM:Orange – noTOM:Green 1.671 TOM:Orchid – noTOM:Brown TOM:Orchid – noTOM:Brown 1.685 TOM:Plum – noTOM:Pink TOM:Plum – noTOM:Pink 1.206 Table S6. Complete set of notation Notation Description
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