Figure 3.

Dynamic Changes in Gene Expression across Sequential Biopsies Identify Pathological Processes during CTVT Regression

(A) Schematic depiction of the changes in expression for the early, progressive, and late genes in the different CTVT phases. The dotted line indicates an expression FC > 10 relative to baseline values in the P phase.

(B) Venn diagram illustrating the overlap between differentially expressed genes across all three comparisons. The diagram explains how differentially expressed genes were classified into three categories: early, late, and progressive.

(C) Pie charts indicating the relative proportion of IPA gene networks within the early, progressive, and late upregulated gene groups of CTVT-5 and their relative proportion within the regressing 7xx CTVTs.

(D and E) Heatmaps of comparative IPA analyses showing the top 30 diseases and biofunction pathways (ex cancer) (D) or canonical pathways (E) for B1, B2, and B3 of CTVT-5 and each individual regressive 7xx CTVTs. Pathways are clustered based on significance (−log10 p value, Fisher's exact test) and similarity.

See also Table S3.