KHAEMENES ACADEMY · BIOLOGY 10 · WEEK 25 · DAY 04

Expression Data: Heatmaps & Fold Change

Read gene-expression data quantitatively without mistaking color scales or fold change for direct protein function.

Safety, privacy and evidence boundary

Use fictional regulatory networks and de-identified expression datasets. Epigenetic examples are not permission to infer trauma, disease, behavior, or inheritance in individuals. Avoid deterministic or transgenerational claims not supported by evidence.

Explicit science instruction

Expression studies may report RNA abundance as normalized counts, relative expression, log values, or fold change. A heatmap visualizes patterns but its colors depend on scaling choices. Two-fold means a ratio of 2, while a decrease to half is 0.5-fold; log2 fold change makes increases/decreases symmetric (+1 and −1).

Worked example with reasoning

Gene A has normalized expression 20 in control and 80 after signal: 4-fold increase, log2 fold change +2. Gene B goes 80→20: 0.25-fold, log2 −2. These values describe RNA abundance under the measurement method.

Guided question

Why must you inspect a heatmap legend before interpreting red versus blue?

Independent work

  1. Calculate four fold changes.
  2. Convert powers of two to log2 fold change.
  3. Interpret a small fictional heatmap.
  4. Name two reasons RNA abundance may not equal protein activity.

Investigation / Data Lab

Gene-regulation network model

Question: How do combinations of regulators change predicted gene expression?

  1. Build a fictional network with one promoter, two activators, one repressor, and an environmental signal.
  2. Create a truth table for at least eight regulator combinations.
  3. Assign predicted expression states or relative expression values using one explicit rule set.
  4. Change one regulatory rule and identify which predictions change.
  5. Compare the model with a supplied expression heatmap and name one mismatch.

Evidence standard: preserve the network diagram, rule set, truth table, and one revision prompted by evidence.

Misconception check

High expression does not automatically mean a gene is more important, and RNA level does not guarantee protein level or activity.

Formative understanding check

20→40 is what fold change?

Worked response

2-fold, corresponding to log2 +1.

Open-book formative practice only; not an official mastery attempt or grade.

Mentor evidence conference

Ask Archaemenes to challenge your information-flow model, sequence reasoning, data interpretation, and limitations.

Open Archaemenes

Teacher guidance

Foundation: use ratio arrows and legend practice. Core: calculate and interpret expression patterns. Extended: compare normalization choices and biological versus technical replication.

Preserve learning evidence

Keep sequence work, models, corrections, and limitations in the matching Week 25 evidence field.