Figure 5

SMARCB1/INI1 expression profile is validated in an independent CRC microarray dataset, cohort I. (A) Volcano plot shows the graphical breakdown of the statistical analysis of SMARCB1/INI1 microarray data; The (x-axis) is the base 2 logarithm of the fold change, and the (Y-axis) is the negative base 2 logarithm of the q value (or adjusted p-value). Thresholds for both the statistical (q < 0.05) and the biological significance are highlighted and assembled in the top left and top right corner of the graph. The fold-changes with significant p values corresponding to SMARCB1/INI1-Neg and SMARCB1/INI1-High tumors (on the vertical axis) show that a 1.5-fold up- or down-regulation in gene expression is equivalent to log-ratios of +0.5 and −0.5; (B) Frequency of the identified subgroups displaying differential SMARCB1/INI1 transcription in the validation series, cohort I, expressed in percentage; (C) Kaplan-Meier survival analysis is carried out taking into account each category; (D) Heat-map of differentially expressed genes. A hierarchical clustering method was used to construct the gene tree as described in Materials and Methods. The lists of differentially expressed genes with a t-test p- value <0.05 including multiple testing corrections were generated (for details, see also Additional file 1: Table S1). Data are shown in a matrix format: each row represents a single gene and each column represents a group. Red indicates overexpressed genes (expression levels over the median) and green indicates underexpressed genes (expression levels below the median; see legend). The pattern and length of the branches in the dendrograms reflect the relatedness of the samples or the genes. The p value is reported in each graph.