Fig. 5

CASC15 knockdown leads to enrichment for the transcriptional program of SOX4 and YY1. a Unsupervised hierarchical gene clustering of differentially expressed genes upon CASC15 siRNA mediated knockdown in RS4;11 cells (PPDE >99%, fold change >2). b-g RT-qPCR confirmation of differentially expressed genes from the microarray in RS4;11 (b-d) and REH (e-g) cell lines. h To narrow down transcription factors that might be responsible for the observed changes in gene expression, we overlapped transcription factors that were associated with the differentially expressed gene sets in CASC15 KD RS4;11 cells as well as CASC15 KO REH cells. Shown are the numbers of genes in the differentially expressed gene set for each transcription factor that showed an association. i-j Enrichment plots from gene set enrichment analysis (GSEA). The differentially regulated gene set from CASC15 KD RS4;11 cells showed a positive enrichment score when compared to genes up-regulated in ACC3 cells with SOX4 knockdown (i; Enrichment Score = 0.5, FDRq = 0.0 and P value = 0.0), and showed a negative enrichment score when compared to genes downregulated in ACC3 cells with SOX4 knockdown (j; Enrichment Score = −0.38,FDRq = .017 and P value = 0.01). k-l Enrichment plots from gene set enrichment analysis (GSEA) showing that the differentially regulated gene set showed a positive enrichment score when compared with upregulated genes upon YY1 knockdown (k; Enrichment Score = 0.5, FDRq = 0 and P value = 0.0) and a negative enrichment score with downregulated genes upon YY1 knockdown (l; Enrichment Score = -0.39, FDRq = 0 and P value = 0.0)