Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells
Figure 7
Identification of the QK and hnRNP A1 regulatory networks in CG-4 cells.
(A) Hierarchical clustering demonstrated high correlation in the gene expression changes between the two knockdown populations. Transcripts altered by QK depletion were identified using a two sample t-test and an FDR of 0.1 (p-value cutoff 0.0012). For the selected transcripts, the expression values of the three biological replicates were averaged and the fold change compared to untransfected CG-4 cells was calculated. The resulting values were clustered (Pearson's dissimilarity, centroid method), and correlation coefficients were calculated. (B) Real time PCR confirmation of microarray results. RNA was extracted from the Qk shRNAmiR knockdown cell line and from the nonsilencing shRNAmiR control cell line. Real time PCR was performed in triplicate. Expression values were normalized to tubulin as a loading control. Data are the mean of three replicates, expressed at log2 for comparison to the microarray results. (C) QK-dependent probeset expression changes are highly correlated with probeset expression changes caused by hnRNP A1 depletion. Individual probesets with expression changes in response to QK knockdown were identified using a two-sample t-test, comparing the knockdown groups to the control groups. The mean of each group was determined and the difference from the CG-4 cell line was calculated. Values were clustered as in (A). Correlation coefficients were calculated using Partek GS software. Probesets were selected for clustering based solely on their change in the QK knockdown samples.