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Figure S1: (A) Table shows number of genes that passed Welchs t-test at different q-values (FDR corrected p-values) and Fold Change cut-offs. (B) Immune.

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Presentation on theme: "Figure S1: (A) Table shows number of genes that passed Welchs t-test at different q-values (FDR corrected p-values) and Fold Change cut-offs. (B) Immune."— Presentation transcript:

1 Figure S1: (A) Table shows number of genes that passed Welchs t-test at different q-values (FDR corrected p-values) and Fold Change cut-offs. (B) Immune system process was identified as the most enriched biological process upon functional enrichment using hypergeometric distribution test with FDR correction (q <0.05), and Fisher Exact Test (p < 0.05) on 1396 RASP regulated transcripts. The immune system process was associated with 177 of 1396 transcripts. Line graph of the177 immune response genes across groups of pre- and post-RASP leukocytes that were also exposed to SEB toxin. Among the 177 transcripts, 26 (red lines) were up-regulated and 151 (blue lines) were down- regulated in post-RASP leukocytes. log fold change RASP + + SEB + + A B

2 Figure S2: Expression changes of genes important for: (A ) pattern recognition receptors, inflammatory response, chemokinesis and activation of myeloid leukocytes; (B) antigen presentation, T-, B- & NK-cells activations; and (C) Transcription regulations. We used two different total RNA isolation methods and different microarray platforms: Trizol RNA isolation and cDNA microarrays (upper panels - purple bar) ; PAXgene RNA isolation and oligonucleotide arrays (lower panels - blue bar). A) B) C)

3 Figure S3: Real time PCR array analyses of transcripts involved in chemotaxis, inflammation, and antigen preparation and presentation pathways. Control (pre-RASP); week 5 (about mid-way of the RASP program); week 8 (post-RASP)

4 A) B) C) D) E) Figure S4: Comparisons of fold changes of transcript levels determined by real time PCR array and cDNA and oligonucleotide microarrays. Shown here are genes significantly associated with: (A) pattern recognition receptors; (B) inflammatory response [to scale the graph, fold changes of and -23.8, labeled * and **, respectively, were assigned a values of ~5 and 6, respectively]; (C) antigen preparation and presentation (*fold change: -12.3; assigned value ~ -5 for scaling the graph); (D) transcription factors (* fold change: -12.6; ** fold change: ; *** fold change: -14; these were adjusted to around -5 for scaling the graph); (E) T-cell activation, differentiation and proliferations. Expression profiles of genes shown in panels A-E were assayed using SABiosciences RT² Profiler (PAHS 406 and PHAS 25) PCR Arrays, cDNA microarrays, and oligonucleotide microarrays. Total RNA samples were isolated using Trizol ® reagents for cDNA microarray analysis, and total RNA samples used for PCR and oligonucleotide arrays were isolated from blood samples collected in PAXgene ® tubes. (Note: Study subject for the PCR arrays were the 10 soldiers who started and completed the RASP).

5 RASP + + SEB + + Figure S5: Expression pattern of RASP suppressed 151 immune response genes in pre- and post-RASP leukocytes which were also exposed to SEB toxin. These is the same data as that of Figure 4A, without linear transformation against pre-RASP control groups

6 Figure S6: (A) Regulatory interaction among stress regulated microRNAs (miRs), important transcription factors (NFkB1, NR3C1, SATB1), inflammatory cytokines and antigen presenting molecules; (B) Seven stress-suppressed miRs targeting 48 mRNAs among 288 mRNAs that passed q < and 1.5 fold change. Enriched pathways include IL-17A and IL-8 signaling, and NFkB activation pathways. A B fold change

7 Figure S7: Transcription factors with absolute z-score > 3.0, and their regulatory targets. Targets were identified among stress altered transcripts (288 transcripts, Fig. 1A) that passed Welchs t-test with FDR correction (q < 0.001) and 1.5 fold change cut off. The left panel shows pathways associated with these genes. fold change

8 Figure S8: Transcription factors targeting transcripts which were differentially regulated among RT-PCR assayed transcripts. Both MYC and NR3C1 were predicted to be activated (according to prediction z-score values, z-score > 2.5). Top functions associated with these targets were apoptosis of leukocytes, hematopoiesis, proliferation of blood cells, and immune response. Top pathways are shown in the table (left panel). fold change

9 Figure S9: Canonical pathways significantly associated with RASP (battlefield-like stress ) regulated genes that passed Welchs t-test and FDR correction (p <= 0.001) and 1.5 Fold change. Numbers on the right side indicate total # of genes in the pathway.


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