Relationships between co-expression modules, cytokines, and differentially expressed gene signatures.

<p><b>A</b>) Association between gene modules and cytokine production, with the color intensity indicating p-value (–log10, BH-adjusted) from linear regression between the modules’ eigengenes and the level of cytokine, and color indicating the correlation direction (red = positive, blue = negative). <b>B)</b> Enrichment of the co-expression modules in differentially expressed gene signatures, with the color intensity indicating p-value (–log10, BH-adjusted) from Fisher’s exact test for modules’ enrichments in the DEG signatures, and color indicating whether the genes in the signature were up-regulated (red) or down-regulated (blue). Module size (number of genes) is indicated in parenthesis after the label; the color scale (p-value) is truncated at ±10 (max is 163).</p

Immune Annotation analysis of the differentially expressed gene signatures.

<p>The color intensity indicates the Immune Annotation Score and the values are the odds ratios from Fisher’s exact tests with BH adjusted p-value < 0.1 for the given test. A. Level 1 (Cells), B. Level 2 (Cell Subsets), C. Level 3 (Activation Status), D. Level 4 (TLR-activated myeloid cells). The color indicates whether the genes in the signature were up-regulated (red) or down-regulated (blue). The results are shown for twelve of the total 24 DEG signatures used in the analysis, and immune Annotation categories with at least a single category with BH adjusted p-value ≤ 0.1. Colored text highlights significant associations with the matching DEG signature. Inf = Infinite, all observations were within the subgroup.</p

Cytokine secretion by group and stimulation condition.

<p>Cytokine secretion by group and stimulation condition.</p

Enrichment of differentially expressed gene signatures for transcription factor targets.

<p>Enrichment of the DEG signatures (top 200 by FC from top 500 by p-values) for transcriptional factor target gene sets, with Chip-X (ChIP-chip, ChIP-seq, ChIP-PET and DamID) derived ChEA set from human based experimental data in <b>A)</b>, ChEA set from rodent based experimental data in <b>B)</b>, and computationally predicted TRANSFACv.1 set in <b>C)</b>. The color intensity indicates–log10 of the FDR adjusted p-values and the indicated values are odds ratios (Fisher’s exact test). The color indicates whether the genes in the signature were up-regulated (red) or down-regulated (blue). The results are shown for only twelve (out of the total of 24 used in the analysis) DEG signatures, and only the TF target sets with at least a single enrichment with BH adjusted p-value ≤0.0001 for A) and B) and ≤0.05 for C), clustered according to the similarity of the enrichment pattern.</p

Immune Annotation enrichment in five egg allergy-associated co-expression modules.

<p>Enrichment results are shown for A) Level 1 immune cell types; B) Level 2 immune cell sub-types; C) Level 3 activation state of immune cell types; and D) Level 4 myeloid cell stimulation. The color intensity indicates the Immune Annotation Score and the values are the Fisher’s exact tests’ Odds Ratios for tests with BH adjusted p-value ≤ 0.10. Only categories with at least one significant result are included. Inf = Infinite, all observations were within the subgroup.</p

Differential expression of interferon response gene sets.

<p>Differential expression of eleven genes from the HALLMARK_ INTERFERON_ALPHA_RESPONSE (including 7 genes also in INTERFERON_GAMMA_RESPONSE, on the left) gene sets overlapping with the DEG signatures (top 200 by FC from top 500 by p-values). Color intensity and values indicate the nominal significance of the differential expression analysis, with values corresponding to negative logarithm of p-values (included for p-values < 0.05). The color indicates whether the genes in the signature were up-regulated (red) or down-regulated (blue).</p

Enrichment of differentially expressed gene signatures in Hallmark functional annotation categories.

<p>Enrichment of selected DEG signatures (top 200 by FC from top 500 by p-values) in Hallmark functional categories, with the color intensity indicating–log10 of the BH adjusted p-value and the values are odds ratios from Fisher’s exact tests. The left 3 signatures indicate EW vs. M for each clinical group, while the right 3 signatures indicate the difference in differential (EW vs. M) gene expression between groups. The color indicates whether the genes in the signature were up-regulated (red) or down-regulated (blue). Hallmark categories with at least a single enrichment with BH adjusted p-value ≤ 0.05 (out of total of 50) are shown, clustered according to the similarity of the enrichment pattern. Colored text highlights significant associations with the matching DEG signature.</p

Top 30 up regulated and down-regulated genes in BER_(EWvs.M) vs. AC_(Ewvs.M) differential expression sorted by fold change.

<p>Top 30 up regulated and down-regulated genes in BER_(EWvs.M) vs. AC_(Ewvs.M) differential expression sorted by fold change.</p