Fig. 7

Analysis of concordance in gene expression changes induced by transcription factor (TF) overexpression and axotomy. (A) Venn diagrams showing the overlap in differentially expressed genes (DEGs) induced in each direction by TF over-expression and by axotomy. DEGs induced at 1 and 7 days after axotomy were pooled for this analysis. In all cases except MEF2 the overlap was significant (p-values given by each diagram; Fisher’s exact test). (B) Correlations of log fold-changes (LFC) induced by TF-expression (with respect to the No-TF vector) and by axotomy (with respect to uninjured neurons) in DEGs induced by axotomy. Correlations are significant for all TF groups except MEF2 (Pearson’s correlation test). Red dots indicate genes also significantly altered by TF overexpression. (C) Converse analysis to B; correlations of LFC induced by axotomy with LFC induced by TF overexpression for all DEGs induced by each TF combination (p-values from Pearson’s correlation test). Green dots indicate genes also significantly altered by axotomy. D, E. Rank-rank hypergeometric overlap analysis of TF induced gene expression changes and axotomy-induced gene expression changes, for all genes. Significance values of the overlaps in the first x and y genes of each list are plotted according to the colour key (after multiple testing correction). Highly significant overlaps are found in the ranked gene lists for each TF group except MEF2, with the ranked gene lists for 7 day axotomy, and to a lesser degree, with the ranked gene lists for 1 day axotomy. For all the analyses shown in A-E, ATF3, KLF7 and ATF3/KLF7 show strong concordance of TF induced changes with axotomy induced changes, while KLF7/MEF2 shows slightly less but still highly significant concordance