Fig. 3.

Alteration of the EGF-regulated transcriptome by SYK knockout. (A) The design and comparative analyses examining differentially expressed genes between OVISE SYK^WT and syngeneic SYK^KO cells in the presence or absence of EGF using RNA-seq. EGF-responsive genes are obtained from comparing SYK^WT cells with and without addition of EGF (50 ng/mL). This comparison is extended to SYK^KO cells to derive EGF-responsive genes in SYK^KO condition, while comparison between SYK^WT and SYK^KO (in the absence of EGF) results in genes that are regulated by SYK. (B) Numbers of differentially expressed genes (FDR <0.01) identified as “SYK-regulated genes”, “EGF-responsive genes” or “EGF-responsive genes in SYK^KO”. (C) Ingenuity Pathway Analysis showing transcriptional network of EGFR-regulated and ERBB2-regulated genes identified among the genes that were differentially expressed between SYK^WT and SYK^KO cells. Upregulated genes are shown in red, and downregulated genes in green. (D) Top canonical signaling pathways that are shared between SYK-regulated and EGF-responsive genes. (E) Function-based analysis of the 712 “SYK-dependent” genes. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)