Additional file 1: of Extensive transcriptomic study emphasizes importance of vesicular transport in C9orf72 expansion carriers
Creators: name: Dickson, Dennis
name: Baker, Matthew
name: Jackson, Jazmyne
name: Mariely DeJesus-Hernandez
name: NiCole Finch
name: Shulan Tian
name: Heckman, Michael
name: Pottier, Cyril
name: Gendron, Tania
name: Murray, Melissa
name: Yingxue Ren
name: Reddy, Joseph
name: Graff-Radford, Neill
name: Boeve, Bradley
name: Petersen, Ronald
name: Knopman, David
name: Josephs, Keith
name: Petrucelli, Leonard
name: Bjรถrn Oskarsson
name: Sheppard, John
name: Asmann, Yan
name: Rademakers, Rosa
name: Marka Van Blitterswijk
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1 a Module-trait relationships are presented for patients with an expanded C9orf72 repeat and patients without this repeat (C9Plus vs. C9Minus). b For patients with an expansion and control subjects (C9Plus vs. Control), module-trait relationships are plotted. These plots are generated with weighted gene co-expression network analysis (WGCNA) to find groups of genes that go up (red) or down (blue) together. A unique color has been assigned to each of these groups, also called a module. Correlations and p-values are shown for variables of interest, including disease group (C9Plus, C9Minus, and/or Control; arrow), neurons, microglia, astrocytes, oligodendrocytes, endothelial cells, RNA integrity number (RIN), age at death, sex, and plate. The strongest correlations (brightest colors) are observed for cell types. Notably, both module-trait relationship plots are based on residuals obtained without adjustment for cell-type-specific markers. Figure S2 a With adjustment for cell-type-specific markers, a cluster dendrogram is shown for C9orf72 expansion carriers and control subjects. b For the same comparison, a cluster dendrogram is displayed without adjustment for cell-type-specific markers. The branches in these dendrograms correspond to specific modules. A unique color has been assigned to each of these modules. Additionally, variables of interest are included, such as the disease group, neurons, microglia, astrocytes, oligodendrocytes, endothelial cells, RNA integrity number (RIN), age at death, sex, and plate. High levels are shown in red and low levels in blue. After adjustment, no striking differences are observed based on cell type; without adjustment, however, modules appear to be associated with certain cell types (e.g., turquoise and neurons). Figure S3 a For patients harboring a C9orf72 repeat expansion and those without this expansion (C9Plus vs. C9Minus; module membership &gt; 0.6 and significance &lt; 1.0E-05), a gene network is displayed. b A gene network is visualized when examining expansion carriers and controls (C9Plus vs. Control; module membership &gt; 0.6 and significance &lt; 1.0E-05). In these network plots, the connectivity of each gene is represented by the size of its node, the module to which it has been assigned by its color, and the strength of the correlation by the thickness of its edges; the C9orf72 gene is denoted by an arrow. Of note, the plots in this figure have been generated without adjustment for cell-type-specific markers. Figure S4 a-d Trends are displayed for patients carrying a C9orf72 repeat expansion. a The first plot shows VEGFA and age at onset. b CDKL1 and C9orf72 expansion size are shown in the second plot. c The third plot displays EEF2K and poly(GP) levels. In these three plots, the solid blue line denotes the linear regression line, while each individual is represented by a solid dark grey circle. d The last plot shows SGSM3 levels and survival after onset, when comparing the bottom 50% (solid salmon line) to the top 50% (solid turquoise line). These plots have been created using residuals unadjusted for differences in cellular composition. Figure S5 a-h The expression levels of VEGFA, CDKL1, EEF2K, and SGSM3 are shown for all disease groups: patients with a C9orf72 repeat expansion (C9Plus), patients without this expansion (C9Minus), and control subjects (Control), both with and without adjustment for cell-type-specific markers. For each box plot, the median is represented by a solid black line, and each box spans the interquartile range (IQR; 25th percentile to 75th percentile). Figure S6 a-h This figure displays the correlation between our expression assays (relative expression) and RNA sequencing data (residuals). a-b The first two plots show correlations for VEGFA, either with or without adjustment for cell-type-specific markers. c-d The next two plots visualize correlations for CDKL1, both with and without adjustment for cellular composition. e-f EEF2K is displayed on the next plots, again with and without adjustment for surrogate markers. g-h The last two plots show correlations for SGSM3 with and without adjustment for cellular composition. For each of these plots, the solid blue line denotes the linear regression line, while each individual is represented by a solid dark grey circle. (PDF 2894 kb)