Supplementary Material: Robust gene coexpression networks using signed distance correlation Javier Pardo-Diaz 1,3,* , Lyuba V. Bozhilova 1 , Mariano Beguerisse-Díaz 2 , Philip S. Poole 3 , Charlotte M. Deane 1 and Gesine Reinert 1,† 1 Department of Statistics, University of Oxford, Oxford, UK 2 Mathematical Institute, University of Oxford, Oxford, UK 3 Department of Plant Sciences, University of Oxford, Oxford, UK * jdiaz@stats.ox.ac.uk † reinert@stats.ox.ac.uk 1 Rhizobium leguminosarum expression data Table S1 provides the details of the gene expression data employed to generate the gene coexpression networks for R. leguminosarum. We used 54 different microarrays obtained under 18 conditions (first column). The second column indicates the growth condition of the bacteria; for example, “7 days pea, 1 day PI" stands for inoculation of seven days old pea plant sampled one day post-inoculation. The last column indicates the type of sample, which can be “Free-living" (bacteria grown in liquid culture), “Rhizosphere" (bacteria isolated from the fraction of soil in contact with the plant), or “Bacteroid" (bacteria that have infected the plant and differentiated). This data has been published previously [8, 6, 3] but never analysed jointly. Microarrays (channels) Growth condition Type kk21 (Cy3), kk41 (Cy5), kk45 (Cy3) Succinate NH 4 Free-living Jay10 (Cy5), Jay11 (Cy5), Jay12 (Cy3) Glucose Glutamate Free-living Jay10 (Cy3), Jay11 (Cy3), Jay12 (Cy5) Glucose Aspartate Free-living kk46 (Cy3), kk48 (Cy3), kk50 (Cy3) Pyruvate NH 4 Free-living Vinoy43 (Cy5), Vinoy44 (Cy5), Vinoy45 (Cy3) Pyruvate NH 4 Hespertin Free-living Ade7 (Cy3), Ade9 (Cy3), Ade18 (Cy5) Pyruvate NH 4 IAA Free-living Ade8 (Cy5), Ade11 (Cy3), Ade15 (Cy5) Pyruvate NH 4 Kinetin Free-living kk39 (Cy5), kk43 (Cy5), kk51 (Cy3) Inositol NH 4 Free-living Vinoy26 (Cy5), Vinoy31 (Cy5), Vinoy34 (Cy3) 7 days pea, 1 day PI Rhizosphere Vinoy27 (Cy5), Vinoy32 (Cy5), Vinoy35 (Cy3) 7 days pea, 3 day PI Rhizosphere Vinoy28 (Cy5), Vinoy33 (Cy5), Vinoy36 (Cy3) 7 days pea, 7 day PI Rhizosphere Vinoy29 (Cy5), Vinoy37 (Cy5), Vinoy39 (Cy3) 14 days pea, 1 day PI Rhizosphere Vinoy30 (Cy5), Vinoy38 (Cy5), Vinoy40 (Cy3) 21 days pea, 1 day PI Rhizosphere kk67 (Cy5), kk71 (Cy3), kk72 (Cy5) 1 week pea, 7 days PI Bacteroid kk65 (Cy5), kk68 (Cy3), kk69 (Cy3) 1 week pea, 15 days PI Bacteroid kk73 (Cy5), kk74 (Cy3), kk75 (Cy5) 1 week pea, 21 days PI Bacteroid kk64 (Cy5), Vinoy22 (Cy3), Vinoy24 (Cy3) 1 week pea, 28 days PI Bacteroid kk70 (Cy5), kk60 (Cy3), kk61 (Cy5) Vetch seed, 28 days PI Bacteroid Table 1: Rhizobium leguminosarum gene expression data description 1 Downloaded from https://academic.oup.com/bioinformatics/article/37/14/1982/6125359 by guest on 10 October 2023