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elapraznik merged 1 commit into from
Apr 23, 2026
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Add additional information in quiz part 3 #12

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6 changes: 4 additions & 2 deletions _chapters/single-cell-analysis/quiz-03/index.md
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Expand Up @@ -23,7 +23,9 @@ title: 'Quiz'
timeout={10}>
</Question>

Perform cluster exploration on the retinal dataset. Use the data table of known marker genes ([sc-quiz-marker-genes.xlsx](http://file.biolab.si/datasets/sc-quiz-marker-genes.xlsx)) for each cell type (don't forget to pass the marker genes data though the Genes widget to annotate!) and set the aggregation parameter in the Score Cells widget to **Fraction of expressed markers**.
Perform cluster exploration on the retinal dataset. Remember, you have already performed quality control and preprocessing steps on it, as well as annotation.

a) Use the data table of known marker genes ([sc-quiz-marker-genes.xlsx](http://file.biolab.si/datasets/sc-quiz-marker-genes.xlsx)) for each cell type (don't forget to pass the marker genes data though the Genes widget to annotate!) and set the aggregation parameter in the Score Cells widget to **Fraction of expressed markers**.

![](sc-ex3-q2.jpg)

Expand Down Expand Up @@ -89,7 +91,7 @@ Liang et al. report that in the peripheral tissue the proportion of rods in comp
</Question>


Select the top 100 genes that are differentially expressed in cones in comparison to non-cones (T-test). Forward them to the GO widget. Sort the lower list by increasing p-value.
Select the top 100 genes that are differentially expressed in cones in comparison to non-cones (T-test). Forward them to the GO widget. Sort the lower list in the GO widget by increasing p-value. Enlarge the window so you see the enhancement scores on the right side. Scroll down and identify the first three GO terms with a high-p value and an an enrichment score above 40 (you can see the numerical enrichment score by hovering over the bar representation of it on the right side of the window).

<Question
id="sc-ex3-q5"
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