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Figure 3 | BMC Research Notes

Figure 3

From: Computational extraction of a neural molecular network through alternative splicing

Figure 3

Pathway analysis of 49 genes whose functional domains were changed by DAS exons. The EGFR/mTOR signaling pathway was analyzed using 49 genes, where the functionalities of the changed domains were related to gene annotations. Thus, representative functions of these genes may be regulated by alternative splicing events. Seven of them were shown with larger fonts with an inner color. The lines indicate the intermolecular relationships. Medium fonts indicate differentially expressed genes suggested by a previous analysis [12]. Outer colors indicate the elevation or reduction of their expressions. Smaller fonts indicate closely related upstream or downstream proteins. Blue or red indicate successfully validated gain of function and elevation of expression or loss of function and reduction of expression, respectively. Success of the validation by semi-quantitative RT-PCR was determined by an Fc value > 1.5 between undifferentiated P19 cells (day 0) and the cells at the neuronal stage (day 7) (see also Figure 4). Light blue or orange colors indicate unsuccessful validation, even though these genes were suggested by a previous microarray experiment. The violet inner color of Kitlg indicates that its domains were suggested to change but the gain or loss of function was difficult to determine. Tsc2 was not one of the extracted 49 genes, but was one of 262 DAS exon genes. Indeed, its alternative isoforms have no difference in their functional protein domains. Additionally, the transcript of p53 (TP53) was not listed as a differentially expressed gene; however, its protein level was likely to be upregulated, as described in a previous report [37].

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