Fig 1.
Worm burden and expression of select genes at mRNA levels detected using quantitative RT-PCR in resistant (RES) and susceptible (SUS) lambs in response to a Trichostrongylus colubriformis challenge infection in sheep.
A. parasite worm counts. B – F: the expression of select transcripts detected using quantitative RT-PCR. Y-axis: transcript copy number expressed as log2 values. B. LGASL15. C. CDC42. D. APOC. E. HSP90B1. F. KRT8. N = 20 per group. * P < 0.05; ** P < 0.01; *** P < 0.001 (based on the Wilcoxon rank sum test).
Fig 2.
Select modules significantly correlated with parasitological traits in the gene interaction network inferred from susceptible lambs in response to T. colubriformis infection.
The color bar on the left represents module names. The numbers denote correlation coefficient values obtained using the biweight mid-correlation (bicor) method (Right). The number in the parenthesis represents the significance (P value). WEC: fecal worm egg counts. N = 20 per group.
Fig 3.
Composite statistics of modules inferred from resistant (RES) lambs that were preserved in susceptible (SUS) lambs.
A. the summary statistic Zsummary (y-axis) as a function of the module size (x-axis). Each dot represents a module as labeled by a color. The dashed lines indicate empirical thresholds for Zsummary values. Any module above the upper dash line with Zsummary > 10 would have strong evidence that the module is preserved; The blue module in the RES network, in this case, was strongly preserved in the SUS network. The Zsummary range between 2 and 10, such as in Module turquoise, indicates that there is weak to moderate evidence of module preservation, whereas Zsummary < 2 suggests that little evidence for module preservation.
Fig 4.
Differentially correlated gene pairs between the SUS and RES groups calculated using Spearman’s rank correlation.
Expression values between CD164 (x-axis) and poly(RC) binding protein 1 (PCBP1; y-axis) in the resistant phenotype (RES, left) and the susceptible lambs (SUS, right) were shown. The grey area represents 95% confidence intervals. The red (left) and blue (right) lines represent a linear model of the best fit. The correlations between CD164 and PCBP1 were strong in resistant (RES) lambs (Spearman’s rho ρ = 0.94, FDR = 2.43 x 10-10), but no correlation in susceptible (SUS) lambs (ρ = 0.31, FDR = 0.18).
Fig 5.
A global view of gene ontology (GO) terms enriched in the set of gene pairs with gain-of-correlation (GOC) in resistant (RES) but not in susceptible (SUS) phenotypes.
Only genes with significant gain-of-correlations at FDR < 0.05 were analyzed using GOstats. Odds ratios (OR) for the GO enrichment of terms were listed. The top ten significantly enriched GO terms from each GO category are shown. The color of GO term bars denotes each of the three GO categories: Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). N = 20 per group.
Fig 6.
Significantly enriched Gene ontology (GO) terms in select modules detected using the DGCA algorithm.
Top: each column represents a module (ME). Left: significantly enriched GO terms at FDR adjusted P-value < 0.01 in select modules. Right: the color panel represents significance threshold (-log10 P value). The color in each cell denotes significance levels. The number in each cell represents odds ratio (OD).
Fig 7.
A differential correlation module from DGCA-MEGENA analysis with most enriched in gene pairs with gain-of-correlation (GOC) in RES lambs.
The sizes of nodes and texts of gene symbols are proportional to the number of connections (correlations) for each gene. Edges are colored according to the differential correlation class as described in the legend (Right), while edge weight is proportional to the absolute value of the z-score for the difference in correlations between the two phenotypes. Three hub genes, olfactory receptor family 2 subfamily AT member 4 (OR2AT4), RAB32, member RAS oncogene family (RAB32), and TNF receptor superfamily member 1A (TNFRSF1A), each correlated with 95, 19, and 16 other genes, respectively, were shown in a large bold font. ρ: Spearman rho correlation coefficient. The plot was made using Cytoscape (v3.10.3).