February 4, 2016

Classwork

Consider how signaling cascades often involve a G-protein, receptor, and ligand. The Burmese Pythons do not always feed, so it is likely that the transcripts for these genes are not always present. Therefore, we are looking for a transcription factor activator because these genes likely turn on a multitude of other genes.

Moving forward, we need to:

• Validate our 12 samples and compare them to one another.
• Identify a housekeeping gene in the Small Intestine mucosa.
• Determine a grouping on the dedrogram and set a threshold.
• Identify genes that will distinguish fed-state from fasted-state.

Questions to Consider:

• When working with large data sets, how do we separate out what is statistically and biologically interesting?

Correlation Activity

• R² value indicates how well the trend line explains the correlation of data. R² is the square of the correlation coefficient.
• Slope indicates if data is positively or negatively related, or if there is no correlation.
• We can practice correlating gene expression across gene samples.
• Correlation deals with rate of change, NOT magnitude of change.
• Subtle changes occurring within a single sample can dramatically change the correlation coefficient.
  • Biologically, it is not uncommon to have a gene that does not change much.

We need to understand "who" the outlier is in our research.

Questions to Consider:

• Knowing subtle changes within a sample can dramatically change the correlation coefficient, should we include all three snakes from each category in a cluster?
• How do we cluster the most effectively?

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