![]() STRING - for networks constructed from a query gene set (e.g., the significantly differentially expressed genes from your data).NDEx - for user network collected from databases and users.Unfortunately, there is not a single "true" network :). The first step in most cases is to identify the source of the network or pathway that you want to work with. There are a few directions you could go with your analysis of expression data in Cytoscape. 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. 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. 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. However, I'm not sure what is the best approach to interpret the results in the context of a biological network. I have visualised their values on the network.
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