I have time series expression data. I have visualised their values on the network. However, I'm not sure what is the best approach to interpret the results in the context of a biological network. I wonder if I should visualise the expression value at the given time or log2 transform data and check the FC between two different experimental conditions at a given time or the difference in FC between the same experimental conditions at two different times. I try to follow the basic expression analysis tutorial but this issue is not described in details and I don't know what is the best approach in order to infer if a transcriptional activation activity of the specific gene is repressed by some other genes.
In the tutorial they have written that "The gal80Rexp expression values will be mapped to node color; nodes with low expression will be colored blue, nodes with high expression will be colored red." but later they had said :"Both nodes (GAL4 and GAL11) show fairly small changes in expression, and neither change is statistically significant: they are pale blue with thin borders. " Thus, I'm puzzled.
I will appreciate any suggestion.