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[…] of 1334 differentially expressed genes. Four pathways were enriched for differentially expressed genes with a false discovery rate (FDR) corrected p-value <0.05, and the majority of these pathways were associated with immune responses (Additional file : Table S1). In agreement with the large number of ISGs identified in the top 100 modulated genes (Figure ), the two pathways containing the greatest enrichment for differentially expressed genes were the Chemokine signaling and Cytokine-cytokine receptor interaction pathways. The fold changes associated with the differentially expressed genes at day 14 post-infection were superimposed on the Chemokine signaling pathway and visualized using Cytoscape (Figure ). Chemokine signaling clearly contributes to the upregulation of ISGs since the following signaling cascade is upregulated at the transcriptional level: Chemokine → Chemokine receptor (R) → JAK2/3 → STAT → ISG expression (Figure )., The identification of gene ontology (GO) terms significantly over-represented in the set of 1334 differentially expressed genes was performed using the Biological Networks Gene Ontology (BiNGO) tool [], which preserves the hierarchical relationship among ontology terms (Figure ). Using an FDR corrected p-value cut-off <0.001 the three most significant GO terms were: immune system process, immune response, and defense response. Therefore, the immune related terms revealed by GO analysis agree with the results obtained from pathway analysis. The entire list of GO terms that were significantly enriched for differentially expressed genes at an FDR corrected p-value <0.05 are available in Additional file : Table S2., Protein-protein and protein-DNA interactions between 416 genes that were differentially expressed between mice strains at day 14 were identified using MetaCore (GeneGo, St. Joseph, MI). The resulting protein interaction network depicted in Figure consists of four major hubs: hypoxia inducible factor 1A (HIF1A), interferon regulatory factor 1 (IRF1), STAT1, and Yin Yang 1 (YY1). These hubs represent transcription factors, which themselves, as well as their targets, were differentially expressed between mouse strains. HIF1A, IRF1, and STAT1, were expressed to a greater extent in DBA/2 compared to C57BL/6 mice, and YY1 to a lesser extent. STAT1 is the largest hub representing the transcription factor regulating the most differentially expressed genes and it was previously selected as a target for RT-qPCR confirmation from the top 100 modulat […]

Pipeline specifications

Software tools Cytoscape, BiNGO, MetaCore