Table 1.
Number of genes and transcript isoforms analyzed and differentially expressed between BCG-challenged (BCG) and Control mice within cell type and between microglia and macrophages within challenge group and overlapping counts.
Table 2.
Most extreme differentially expressed genes between BCG-challenged and Control mice within microglia (|log2(fold change)| > 3, FDR-adjusted P-value < 2.0 x 10−3) and macrophages (|log2(fold change)| > 6, FDR-adjusted P-value < 3.0 x 10−4) and supporting literature review.
Table 3.
Most significant clusters (DAVID Enrichment Score ES > 4) of enriched Gene Ontology (GO) biological processes (BP) and molecular functions (MF) among the genes differentially abundant between BCG-challenged and Control mice within cell type.
Table 4.
Gene Set Enrichment Analysis (GSEA) categories enriched among transcript isoforms over-expressed (FDR-adjusted P-value < 5.0 x 10−4 > 10 transcript isoforms) and under-expressed (P-value < 0.05 > 10 transcript isoforms) in BCG-challenged relative to Control mice in microglia.
Table 5.
Gene Set Enrichment Analysis (GSEA) categories enriched among transcript isoforms over-expressed (FDR-adjusted P-value < 1.5 x 10−2 > 10 transcript isoforms) and under- expressed (FDR-adjusted P-value < 5 x 10−4 > 10 transcript isoforms) in BCG-challenged relative to Control mice in macrophages.
Fig 1.
Network of genes differentially expressed between BCG-challenged and Control mice in microglia.
Red (green) nodes denote genes over- (under-) expressed in BCG-challenged relative to Control mice. Node size represents the P-value were larger nodes indicates more extreme significance (FDR-adjusted P-value < 0.001 larger nodes; P-value < 0.05 intermediate nodes; P-value < 0.1 small nodes). Edges denote known relationships between genes in the SysBiomics repository. Framed genes (squares) are discussed in the manuscript.
Fig 2.
Network of genes differentially expressed between BCG-challenged and Control mice in macrophages.
Red (green) nodes denote genes over- (under-) expressed in BCG-challenged relative to Control mice. All genes were differentially expressed at FDR-adjusted P-value < 0.001. Edges denote known relationships between genes in the SysBiomics repository. Framed genes (squares) are discussed in the manuscript.
Table 6.
Most extreme differentially expressed genes (FDR-adjusted P-value < 2.0 x 10−4) between microglia and macrophages in BCG-challenged mice and supporting literature review.
Table 7.
Most significant clusters (DAVID Enrichment Score ES > 4) of enriched Gene Ontology (GO) biological processes (BP) and molecular functions (MF) among the transcript isoforms differentially abundant between microglia and macrophages from BCG-challenged mice.
Table 8.
Gene Set Enrichment Analysis (GSEA) categories enriched (FDR-adjusted P-value < 0.01, > 10 transcript isoforms) among transcript isoforms under-expressed in microglia relative to peripheral macrophages in BCG-challenged mice.
Table 9.
Genes exhibiting an alternative splicing event between microglia and macrophages in BCG-challenged mice including at least nine transcript isoforms and at least two over- or under-expressed (FDR-adjusted P-value < 0.05) transcript isoforms between cell types.
Fig 3.
Network of genes differentially expressed between microglia and macrophages in BCG-challenged mice.
Red (green) nodes denote genes over- (under-) expressed in BCG-challenged relative to Control mice. All genes were differentially expressed at FDR-adjusted P-value < 0.0001. Edges denote known relationships between genes in the SysBiomics repository. Framed genes (squares) are discussed in the manuscript.