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Fig. 3 | BMC Medical Genomics

Fig. 3

From: Transcriptomic biomarker pathways associated with death in HIV-infected patients with cryptococcal meningitis

Fig. 3

Comparisons of the expression of immune genes and immune/inflammatory pathways between groups. a–e Biofunction heatmap illustrations of pathway-level enrichment based on ANOVA analysis are shown. IPA software was used to visualize differences in enrichment of transcripts that are involved in canonical pathways. The heatmaps display top up- and down-regulated pathways. The color of heatmap squares represents the activity of biofunctions. The z-scores represent the significance of fold changes in expressions and colored as activation z-score > 2 (orange squares), repression z-score < -2 (blue), and insignificant z-score (white squares). Dots mark the squares which did not pass Benjamini–Hochberg restrictions for changes in gene expression within the canonical pathway. vs., versus. The ranges of z-scores identified in this analysis are between − 3.7 and + 3.7. a. Upregulation of immune pathways in the Fatal C-IRIS Group at week 0. 1. Column 1. Fatal C-IRIS Group versus No C-IRIS or Death Group (control) from both study arms. 2. Fatal C-IRIS Group versus C-IRIS Survivor Group. 3. Fatal C-IRIS Group versus Death without C-IRIS Group. b. Changes in pathway expression at one week after ART initiation as compared to corresponding week 0. 1. Death without C-IRIS Group, week 1 versus week 0 (earlier ART arm). Column 2. Death without C-IRIS Group, week 1 versus week 0 (deferred ART arm). Column 3. Fatal C-IRIS group, week 1 versus week 0 (earlier ART arm). Column 4. No C-IRIS or death Group week 1 verus week 0 (earlier ART arm). Column 5. No C-IRIS or death Group week 1 versus week 0 (deferred ART arm). Column 6. C-IRIS Survivors Group week 1 versus week 0 (earlier ART arm). Column 7. C-IRIS Survivors Group week 1 versus week 0 (deferred ART arm). c Pathway expression comparisons between Groups, at 1 week post-ART (earlier and deferred arms combined). Column 1. Death without C-IRIS Groups versus No C-IRIS or Death Groups (controls). Column 2. Fatal C-IRIS Groups versus No C-IRIS or Death Groups (controls). Column 3. Fatal C-IRIS Group versus Death without C-IRIS Groups. Column 4. C-IRIS Survivor Groups versus Death without C-IRIS Groups. d Changes in pathway expression at 8 weeks after ART initiation. Column 1. Earlier ART arm: No C-IRIS or Death Group (control), week 8 versus No C-IRIS or Death Group (control), week 0 and 4 combined. Column 2. Deferred ART arm: No C-IRIS or Death Group (control), week 8 versus No C-IRIS or Death Group (control), week 0 and 4 combined. Column 3. Earlier ART arm: C-IRIS Survivor Group, week 8 versus C-IRIS Survivor Group at the time of C-IRIS event. Column 4. Deferred ART arm: C-IRIS Survivors Group, week 8 versus C-IRIS survivor Group at time of C-IRIS event. e Immune pathways that were up-down-regulated at the time of C-IRIS events in the earlier arm. Column 1. Fatal C-IRIS Group (event) versus Fatal C-IRIS Group, 1 week (most proximal time point to the event). Column 2. Fatal C-IRIS Group (event) versus No C-IRIS or Death Group (control) at 1 week post-ART. Column 3. Fatal C-IRIS Group (event) versus No C-IRIS or Death Group at week 4 post-ART. Column 4. Fatal C-IRIS Group (event) versus C-IRIS Survivor Groups (event). Column 5. Fatal C-IRIS Group (event) versus Death without C-IRIS Group at week 1.

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