Differential gene expression

Up or down regulation is a contrast between two groups (in this case sick versus healthy). Describe the group comparisons when stating whether genes are up or down-regulated.

Data analysis and presentation

  1. PCAs were over-interpretted.

    • Generally, PCA can represent the overall gene expression

      • by specifically decomposing the variation in the whole transcriptomic response into less variables (PCs).

    • Each individual sample has a value for the new variables (PCs) and you can compare (qualitatively) whether individuals are grouped based on treatment or identity (healthy or sick)

    • So simply state the qualitative pattern of whether groups were generally clustered together or not.

    • One thing to keep in mind is that the overall gene expression response may not differ, but individual transcripts can differ.

  2. Few students noted the low sample size for making the contrast between sick vs. healthy in the subtidal location.

  3. Reference figures when explaining results in the text.

Writing Style

The style of writing should be formal and similar to that of the published articles we have been reading.

Here is a set of suggestions to improve writing:

  1. Avoid lists and write a narrative instead.
    • Write by leading with the biology first and then the statistics support your biological claims.
  2. Use precise language
    • Avoid phrases such as:
    • “look at” when you mean “comparing”
    • and “This is interesting” or “XYZ is interesting”. Make a specifiic argument. i.e. “XYZ suggests that…”
  3. Favor the active voice and keep the verb close to the subject. The active voice naturally creates a narrative because it is analogous to characters performing some action.
    • Passive construction: There were differences in gene expression between sick and healthy individuals.
    • Active construction: Healthy individuals up-regulated 50 genes to a higher degree than sick individuals.
  4. A strategy to present methods is to first provide a justification.
    • In order to characterize differences in the transcriptome, RNA was first isolated using the manufacturer’s instructions and prepared in a library for Illumina sequencing.