File S1 - Systems Biology Analysis of Brucella Infected Peyer's Patch Reveals Rapid Invasion with Modest Transient Perturbations of the Host Transcriptome

Supplemental figures and tables. Figure A in File S1. Validation of Bovine Microarray Results by Quantitative Real Time-PCR. cDNA was synthesized from the same RNA samples used for microarray hybridization. Five randomly selected genes (A  =  BPI; B  =  MAPK1; C  =  MIF; D  =  CCL2; E  =  IL8.) that were differentially expressed by microarrays in B. melitensis-infected bovine Peyer's patch between 15 min and 4 h p.i. as compared to non-infected tissues (control) extracted at the same time points, were validated by quantitative RT-PCR. Fold changes was normalized to the expression of GAPDH and calculated using the ΔΔCt method. All tested genes at all time points had fold-changes altered in the same direction in microarray and qRT-PCR. White bars represent fold-change by microarray analysis and black bars represent fold-change by qRT-PCR. Table S1 in File S1. Detailed List of Host Genes with Differential Expression (z-score >|2.24|) in B. melitensis Infected vs. Control Bovine Jejunal-Ileal Peyer's Patch in at least one time point. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S2 in File S1. Bayesian z-score for All Host Pathways in B. melitensis Infected vs. Control Bovine Jejunal-Ileal Peyer's Patch. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S3 in File S1. List of All Biological Process-Related Host Genes Differentially Expressed in B. melitensis Infected vs. Control Bovine Jejunal-Ileal Peyer's Patch. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S4 in File S1. List of All Cellular Component-Related Host Genes Differentially Expressed in B. melitensis Infected vs. Control Bovine Jejunal-Ileal Peyer's Patch. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S5 in File S1. List of All Molecular Function-Related Host Genes Differentially Expressed in B. melitensis Infected vs. Control Bovine Jejunal-Ileal Peyer's Patch. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S6 in File S1. Group 1 - GO Biological Process Terms Significantly Perturbed Early (Activated or Repressed) but Not Later. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S7 in File S1. Group 2 - GO Biological Process Terms Consistently Perturbed (Activated or Repressed) Throughout the Experiment; Not Significantly Perturbed Early but Later; or Consistently Altered Perturbation (Activated to Repressed or Vice Versa). Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S8 in File S1. Group 1 - GO Cellular Components Terms Significantly Perturbed Early (Activated or Repressed) but Not Later. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S9 in File S1. Group 2 - GO Cellular Component Terms Consistently Perturbed (Activated or Repressed) Throughout the Experiment; or Terms Not Significantly Perturbed Early but Later; or Consistently Altered Perturbation (Activated to Repressed or Vice Versa). Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S10 in File S1. Group 1 - GO Molecular Function Terms Significantly Perturbed Early (Activated or Repressed) but Not Later. Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S11 in File S1. Group 2 - GO Molecular Function Terms Consistently Perturbed (Activated or Repressed) Throughout the Experiment; or Terms Not Significantly Perturbed Early but Later; or Consistently Altered Perturbation (Activated to Repressed or Vice Versa). Black numbers in the body of the table indicate differentially expressed (activated: (+) numbers; repressed: (−) numbers) while red numbers represent non-differentially expressed genes. Table S12 in File S1. Comparative Table of Group 1 and Group 2 Gene Ontology Terms Clustered to the Top 15 Primary Immune Related Biological Process Categories. This table shows lists the mapping of perturbed GO term gene groups to their higher level GO category definitions. The number of perturbed GO terms that mapped to each category is provided in the Count column. Table S13 in File S1. Group 1 - Detailed Listing of the Top 15 Highly Perturbed Gene Ontology Terms Mapped to Major Immune Related Biological Process. This table lists each GO term that was mapped (clustered) to a main category related to an immune response. There were 108 main categories to which 686 perturbed GO term sets of genes resulted in mapping to 55 categories. Group 1 represents those GO terms that were significantly perturbed at earlier time points (either activated or repressed) but not at later time points. Table S14 in File S1. Group 2 - Detailed Listing of the Top 15 Highly Perturbed Gene Ontology Terms Mapped to Major Immune Related Biological Process. This table lists each GO term that was mapped (clustered) to a main category related to an immune response. There were 108 main categories to which 114 perturbed GO term sets of genes resulted in mapping to 23 categories. Group 2 are GO terms consistently perturbed (up- or down-regulated) throughout the experiment; or GO terms not significantly perturbed at earlier time points but at later times; or GO terms that consistently changed their state of perturbation (from activated- to repressed or vice versa). Table S15 in File S1. Comparative Table of Group 1 and Group 2 Gene Ontology Terms Clustered to Primary Cellular Component Categories. The mapping of terms in this table is to major categories related to the cellular component categories. Table S16 in File S1. Group 1 - Detailed Listing of Highly Perturbed Gene Ontology Terms Mapped to Major Cellular Component Categories. This table lists each GO term that was mapped (clustered) to a main category related to its cellular component association. There were 12 main categories to which 112 perturbed GO term sets of genes resulted in mapping to 9 categories. Definition of Group 1 is same as described in Table S13. Table S17 in File S1. Group 2 - Detailed Listing of Highly Perturbed Gene Ontology Terms Mapped to Major Cellular Component Categories. This table lists each GO term that was mapped (clustered) to a main category related to its cellular component association. There were 12 main categories to which 26 perturbed GO term sets of genes resulted in mapping to 6 categories. Definition of Group 2 is same as described in Table S14. Table S18 in File S1. Comparative Table of Group 1 and Group 2 Gene Ontology Terms Clustered to Primary Molecular Function Categories. The mapping of terms in this table is to major categories related to the primary molecular function categories. Table S19 in File S1. Group 1 - Detailed Listing of Highly Perturbed Gene Ontology Terms Mapped to Major Molecular Function Categories. This table lists each GO term that was mapped (clustered) to a main category related to its cellular component association. There were 17 main categories to which 220 perturbed GO term sets of genes resultedin mapping to 10 categories. Definition of Group 1 is same as described in Table S13. Table S20 in File S1. Group 2 - Detailed Listing of Highly Perturbed Gene Ontology Terms Mapped to Major Molecular Function Categories. This table lists each GO term that was mapped (clustered) to a main category related to its cellular component association. There were 17 main categories to which 38 perturbed GO term sets of genes resulted in mapping to 6 categories. Definition of Group 1 is same as described in Table S14. Table S21 in File S1. Mechanistic Genes with Overlapping Intersections among Multiple Pathways. This table lists 476 unique mechanistic genes associated with the list of pathways in Table 2. The table shows the number of pathways for which each gene has an intersection. The Bayesian z-score by time point is provided for each gene. Table S22 in File S1. Significantly Down-Regulated Mechanistic Genes with Bayesian z-score <−2.24 in the Early Stage of Infection (15, 30, & 60 minutes post-infection). The table lists significantly perturbed down-regulated genes with a high degree of overlap (intersection or cross-talk) across multiple pathways (5 or more intersections) associated
with those pathways listed in Table 2. Significant down-regulated Bayesian z-scores in the first hour p.i. are bolded. Table S23 in File S1. Significantly Up-Regulated Mechanistic Genes with Bayesian z-score >2.24 in the Early Stage of Infection (15, 30, & 60 minutes post-infection). The table lists significantly perturbed up-regulated genes with a high degree of overlap (intersection or crosstalk) across multiple pathways (5 or more intersections) associated with those pathways listed in Table 2. Significant up-regulated Bayesian z-scores in the first hour p.i. are bolded. Table S24 in File S1. Description of the Biological Role of Dominant Down-Regulated Mechanistic Genes in Tight Junction Pathway. Table S25 in File S1. Description of the Biological Role of Dominant Down-Regulated Mechanistic genes in Trefoil Factors Initiated Mucosal Healing. Table S26 in File S1. Significant Perturbed Genes and Their Biological Roles for the Lectin Pathway. Table S27 in File S1. Significant Perturbed Genes and Their Biological Roles for Phagocytosis Gene Ontology Group. Table S28 in File S1. Interleukin Mechanistic Genes Significantly Perturbed at 15 minutes post-infection.
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