Correlation of module memberships versus gene significance for disease status.

<p>Scatterplot graphs show the correlation of module memberships of the genes in each module versus significance of the genes for the disease status. Additionally, expression status of the module members was considered and shown in the form of single bar graphs on the right of counterpart scatterplot graphs. Red and blue colors mean down- and up-regulation. Finally, common genes among the modules were presented in Venn diagram graphs below the related scatterplots of all cell types. No common genes were detected among modules of a cell type. a, b, c) modules of DCs. d, e, f) modules of NTs. g, h, i) modules of PBMCs. Abbreviations: DEGs: Differentially Expressed Genes; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

Heat maps of module eigengenes relationships with traits.

<p>a) heat map for the traits of dendritic cells, b) heat map for the traits of neutrophils, and c) heat map for the traits of peripheral blood mononuclear cells.</p

Networks extracted from highly correlated modules to disease.

<p>Using top 10 percent hub genes from the modules we constructed networks of each module and detected DEGs among them. Edges were decreased to leave only about top 25 percent weighted edges. Ticker edge means higher weight. Red and blue colors of nodes show either down- and up-regulated genes, respectively. Venn diagrams at below the networks show common genes in the networks from different cells. No common genes were detected among networks of a cell type. a, b, c) networks of DCs. d, e, f) networks of NTs. g, h, i) networks of PBMCs. Abbreviations: DEGs: Differentially Expressed Genes; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

TFs and GRN analysis.

<p>a) Detected TFs in all cell types and their expression status. Blank spaces mean no expression alteration was observed for the TFs. b) Venn diagram of common TFs among cell types. c) GRN of DCs, d) GRN of NTs, and f) GRN of PBMCs. Blue colors mean up-regulation and red mean down-regulation. Abbreviations: TFs: Transcription Factors; GRN: Gene Regulatory Networks; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

Gene ontology of the DEGs.

<p>Top 10 biological process and top 5 KEGG pathway are presented for a) DCs, b) NTs, and c) PBMCs. Abbreviations: DEGs: Differentially Expressed Genes; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

DEGs involved in inflammatory/immune response.

<p>This table was provided by checking the differentially expressed hub genes in all networks for being involved in inflammatory/immune response. In addition, we checked to datasets to detect if hub genes in this study are also deregulated in others. Abbreviations: PPI: Protein-Protein Interaction; WGCNA: Weighted Gene Co-expression Network Analysis; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

PPI networks and module annotations.

<p>PPI networks of the cell types are presented. Numbers and colorful shades indicate the modules detected by overlapping neighborhood expansion. Tables show the annotation and <i>p-values</i> of the modules corresponding to the networks. a, b) Network and counterpart table of annotations for DCs, c, d) Network and counterpart table of annotations for NTs, and e, f) Network and counterpart table of annotations for PBMCs. Abbreviations: DEGs: Differentially Expressed Genes; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

The count and percentage of DEGs in each cell types.

<p>Top 5 biological processes of both up-and down-regulated genes related to each type of cells are presented in right of the bars. Abbreviations: DEGs: Differentially Expressed Genes; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.</p

Snapshot of GSEA enrichment result related to biological process detected in AD.

<p>Snapshot of GSEA enrichment result related to biological process detected in AD.</p

Snapshot of GSEA enrichment result related to molecular function detected in AD.

<p>Snapshot of GSEA enrichment result related to molecular function detected in AD.</p