DOI: 10.6084/m9.figshare.26563348
title: Additional file 5 of Early peripheral blood gene expression associated with good and poor 90-day ischemic stroke outcomes

description: Additional file 5: Table S1 A Gene expression of genes at ≤ 3 h of ischemic stroke (IS) onset that associates with 90-day outcome. 467 Genes significantly differentially expressed between Poor 90-day mRS IS Outcome and Vascular Risk Factor Control (VRFC) (FDR &lt; 0.05, |FC|&gt; 2). 49 Genes significantly differentially expressed between Good 90-day mRS IS Outcome and VRFC (FDR &lt; 0.05, |FC|&gt; 2). 709 Genes (at ≤ 3 h) significantly differentially expressed between participants with Poor 90-day mRS IS Outcome and participants with Good 90-day mRS Outcome (P &lt; 0.05, |FC|&gt; 1.3). 538 Genes significantly associated with 90-day NIHSS Outcome (P &lt; 0.005) B Gene expression of genes at 5 h of IS onset that associates with 90-day outcome. 526 Genes significantly differentially expressed between Poor 90-day mRS IS Outcome and VRFC (FDR &lt; 0.05, |FC|&gt; 2). 100 Genes significantly differentially expressed between Good 90-day mRS IS Outcome and VRFC (FDR &lt; 0.05, |FC|&gt; 2). 658 Genes significantly differentially expressed between Poor 90-day mRS IS Outcome and Good 90-day mRS Outcome (P &lt; 0.05, |FC|&gt; 1.3). 197 Genes significantly associated with 90-day NIHSS Outcome (P &lt; 0.005). C Gene expression of genes at 24 h of IS onset that associates with 90-day outcome. 571 Genes significantly differentially expressed between Poor 90-day mRS IS Outcome and VRFC (FDR &lt; 0.05, |FC|&gt; 2). 35 Genes significantly differentially expressed between Good 90-day mRS IS Outcome and VRFC (FDR &lt; 0.05, |FC|&gt; 2). 363 Genes significantly differentially expressed between Poor 90-day mRS IS Outcome and Good 90-day mRS IS Outcome (P &lt; 0.05, |FC|&gt; 1.3). 147 Genes significantly associated with 90-day NIHSS Outcome (P &lt; 0.005). D Genes consistently differentially expressed between ischemic stroke participants with poor 90-day mRS outcome and controls over the three time-points. E Genes consistently differentially expressed between ischemic stroke participants with good 90-day mRS outcome and controls over the three time-points. F Genes consistently differentially expressed between ischemic stroke participants with poor vs. good 90-day mRS outcome over the three time-points. G Genes consistently associated with 90-day NIHSS outcome over the three time-points. Table S2 A IPA Canonical Pathway Enrichment (P &lt; 0.05) for gene expression at ≤ 3 h of ischemic stroke (IS) onset that associates with 90-day outcome. IPA Canonical Pathway Enrichment for 467 Genes Significant to Poor 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for 49 Genes Significant to Good 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for 709 Genes Significant to Poor 90-day mRS Outcome vs. Good 90-day mRS Outcome. IPA Canonical Pathway Enrichment for 538 genes associated with 90-day NIHSS Outcome. B IPA Canonical Pathway Enrichment (P &lt; 0.05) for gene expression at 5 h of IS onset that associates with 90-day outcome. IPA Canonical Pathway Enrichment for 526 Genes Significant to Poor 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for 100 Genes Significant to Good 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for 658 Genes Significant to Poor 90-day mRS Outcome vs. Good 90-day mRS Outcome. IPA Canonical Pathway Enrichment for 197 genes associated with 90-day NIHSS Outcome. C IPA Canonical Pathway Enrichment (P &lt; 0.05) for gene expression at 24 h of IS onset that associates with 90-day outcome. IPA Canonical Pathway Enrichment for the 571 Genes Significant to Poor 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for the 35 Genes Significant to Good 90-day mRS Outcome as compared to VRFC. IPA Canonical Pathway Enrichment for the 363 Genes Significant to Poor 90-day mRS Outcome vs. Good 90-day mRS Outcome. IPA Canonical Pathway Enrichment for the 147 genes associated with 90-day NIHSS Outcome. D IPA Canonical Pathway Enrichment (P &lt; 0.05) for genes consistently differentially expressed between ischemic stroke participants with poor 90-day mRS outcome compared to controls over the three time-points. E IPA Canonical Pathway Enrichment (P &lt; 0.05) for genes consistently differentially expressed between ischemic stroke participants with good 90-day mRS outcome compared to controls over the three time-points. F IPA Canonical Pathway Enrichment (P &lt; 0.05) for genes consistently differentially expressed between ischemic stroke participants with poor vs. good 90-day mRS outcome over the three time-points. G IPA Canonical Pathway Enrichment (P &lt; 0.05) for genes consistently associated with 90-day NIHSS outcome over the three time-points. Table S3 A DAVID Gene Ontology Enrichment (FDR P &lt; 0.05) for the 467 Genes (at ≤ 3 h) Significant to Poor 90-day Outcome as compared to VRF Controls. B DAVID Gene Ontology Enrichment (FDR P &lt; 0.05) for the 571 Genes (at 24 h) Significant to Poor 90-day Outcome as compared to VRF Controls. Table S4 Hub genes in outcome-associated co-expression modules at 5 h and 24 h from stroke onset. Probe sets without annotated genes are excluded. A 5 h from Stroke Onset. B 24 h from Stroke Onset. Table S5 A IPA Canonical Pathway Enrichment (P &lt; 0.05) for outcome-significant WGCNA modules using gene expression at ≤ 3 h from IS onset. 3hDarkGrey Significant to NIHSS at 90 day. 3hDarkGrey Significant to mRS at 90 day. 3hGreen Significant to NIHSS at 90 day. 3hMidnightBlue Significant to NIHSS at 90 day. 3hMidnightBlue Significant to mRS at 90 day. 3hOrange Significant to mRS at 90 day. 3hPink Significant to mRS at 90 day. 3hPurple Significant to mRS at 90 day. 3hRed Significant to mRS at 90 day. 3hRoyalBlue Significant to mRS at 90 day. 3hRoyalBlue Significant to NIHSS at 90 day. B IPA Canonical Pathway Enrichment (P &lt; 0.05) for outcome-significant WGCNA modules using gene expression at 5 h from IS onset. 5hCyan Significant to mRS at 90 day. 5hDarkOrange Significant to mRS at 90 day. 5hDarkRed Significant to mRS at 90 day. 5hGreenYellow Significant to NIHSS at 90 day. 5hLightCyan Significant to mRS at 90 day. 5hLightGreen Significant to NIHSS at 90 day. 5hLightYellow Significant to mRS at 90 day. 5hRed Significant to NIHSS at 90 day. C IPA Canonical Pathway Enrichment (P &lt; 0.05) for outcome-significant WGCNA modules using gene expression at 24 h from IS onset. 24hGreenYellow Significant to NIHSS at 90 day. 24hOrange Significant to NIHSS at 90 day. 24hPink Significant to NIHSS at 90 day. 24hYellow Significant to mRS at 90 day. Table S6 A IPA Canonical Pathway Enrichment (P &lt; 0.05) for some cell-specific WGCNA hubs at ≤ 3 h. T cell receptor and other T cell-specific Hub Genes. Neutrophil-specific Hub Genes. B IPA Canonical Pathway Enrichment (P &lt; 0.05) for some cell-specific WGCNA hubs at 5 h. T cell receptor and other T cell-specific Hub Genes. Neutrophil cell-specific Hub Genes. C IPA Canonical Pathway Enrichment (P &lt; 0.05) for some cell-specific WGCNA hubs at 24 h. T cell receptor and other T cell-specific Hub Genes. Neutrophil cell-specific Hub Genes. Monocyte cell-specific Hub Genes. Table S7 The 10 genes used as predictors of Poor and Good 90-day mRS Outcomes. Table S8 Genes regulated by tPA in a rat stroke model (Jickling et al., 2010) overlapped with the 5 h and 24 h outcome genes in this study. The only significant overlap of tPA genes with outcomes genes was for 5 h good outcome vs VRFC (P = 0.005).