John Hay
John Hay Biomedical
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Genetics of Disease (Medical Interventions)
Unit 2: Unit 2.1 Gene ExpressionMI 2.1Biotechnology Research and Experiments

Interpret An Expression Heat Map

Read an expression heat map using the legend (red = high, blue = low) to tell which gene is up or down in a sample.

Builds on (2 levels back)inferred · high confidence
  • Control logic: Molecular results need positive and negative controls.
  • Signal interpretation: Bands, colors, curves, and E-values must be compared to a rule.

Prerequisites are inferred: pending teacher review.

Re-learn the skill with worked practice and clear examples.

Read which gene is up or down in a sample by comparing its colored cells against the legend.

Step 1: Pick a gene row
Each row is one gene across the samples. Compare the Tumor cell to the Normal cell for that gene.
Expression heat map. Legend: red = high expression, blue = low. Columns: Tumor and Normal. Gene 1 is red in Tumor and blue in Normal (high in tumor, low in normal). Gene 2 is blue in Tumor and red in Normal (low in tumor, high in normal). Gene 3 is red in both Tumor and Normal (high in both).
Step 2: Translate the colors
Red in Tumor + blue in Normal means the gene is UP in the tumor. Blue in Tumor + red in Normal means it is DOWN in the tumor.
Step 3: Name the limit
A heat map shows that expression differs; it does not by itself prove the gene causes the disease.
Practice

In the heat map, Gene 1 is red in the Tumor column and blue in the Normal column. Compared with normal tissue, Gene 1 in the tumor is:

Reviewed
Expression heat map. Legend: red = high expression, blue = low. Columns: Tumor and Normal. Gene 1 is red in Tumor and blue in Normal (high in tumor, low in normal). Gene 2 is blue in Tumor and red in Normal (low in tumor, high in normal). Gene 3 is red in both Tumor and Normal (high in both).
  1. A.Up-regulated (higher in the tumor)
  2. B.Down-regulated (lower in the tumor)
  3. C.Expressed the same in both
  4. D.Turned completely off in the tumor
Show the worked solution ▾

Answer: A. Up-regulated (higher in the tumor)

  1. Step 1: Read both cells: Tumor cell = red (high); Normal cell = blue (low).
  2. Step 2: Compare: High in tumor and low in normal means Gene 1 is up-regulated in the tumor.

Why it's right: Red (high) in tumor versus blue (low) in normal means Gene 1 is up-regulated in the tumor.

Why the others miss:
  • B: Down-regulated would be blue in tumor, red in normal: that is Gene 2.
  • C: Same would be the same color in both columns.
  • D: 'Red' means high expression, not off.

Aligned to Biotechnology Research and Experiments · reading level ~grade 9

Which gene is DOWN-regulated in the tumor (lower in tumor than in normal tissue)?

Reviewed
Expression heat map. Legend: red = high expression, blue = low. Columns: Tumor and Normal. Gene 1 is red in Tumor and blue in Normal (high in tumor, low in normal). Gene 2 is blue in Tumor and red in Normal (low in tumor, high in normal). Gene 3 is red in both Tumor and Normal (high in both).
  1. A.Gene 2 (blue in Tumor, red in Normal)
  2. B.Gene 1 (red in Tumor, blue in Normal)
  3. C.Gene 3 (red in both columns)
  4. D.None of the genes change
Show the worked solution ▾

Answer: A. Gene 2 (blue in Tumor, red in Normal)

  1. Step 1: Down means low in tumor: Look for blue (low) in the Tumor column and red (high) in Normal.
  2. Step 2: Find it: Gene 2 is blue in Tumor and red in Normal, so it is down-regulated in the tumor.

Why it's right: Gene 2 is blue (low) in the tumor and red (high) in normal, which is down-regulation in the tumor.

Why the others miss:
  • B: Gene 1 is the opposite: up in the tumor.
  • C: Gene 3 is red in both, so it does not change between samples.
  • D: Gene 1 and Gene 2 both change, so 'none' is wrong.

Aligned to Biotechnology Research and Experiments · reading level ~grade 9

Where you'd see this
  • In Unit 2.1 Gene Expression, this skill turns class evidence into a result another person can check.
Careers that use this
Molecular Technologist: Uses interpret an expression heat map to make a decision from evidence without overclaiming.
Video library
Watch: Interpret An Expression Heat Map
Hybridization (microarray) | Biomolecules | MCAT | Khan Academy
khanacademymedicine · ~9 min
Guided notes

Fill these in as you work through the lesson.

Big idea: A heat map's legend turns each colored cell into an expression level; comparing a gene's cells across samples tells you if it is up or down.
Key terms: write the meaning
  • Heat map (grid of cells colored by value):  
  • Legend (key that says what each color means):  
  • Up-regulated (expressed higher in one sample):  
  • Cluster (genes/samples that behave the same group together):  
The rule

Use the legend: red =   expression and blue =   expression; compare a gene's Tumor cell to its Normal cell to tell if it is  .

Check yourself
  1. What does a red cell mean here? A blue cell? 
  2. How do you tell if a gene is up or down in the tumor? 
  3. Why can't a gene that is high in BOTH samples separate them? 
Work one example

For Gene 1 (red Tumor, blue Normal), Gene 2 (blue Tumor, red Normal), and Gene 3 (red both), label each as up, down, or unchanged in the tumor.