DeepCpG Quiz

Which of the following is NOT true about CpG sites?

• CpG stands for cytosine-phosphate-guanine.

• DNA methylation is primarily found at CpG sites.

• Incomplete CpG coverage limits single-cell methylation analyses.

• CpG is named in the 3’ -> 5’ direction.

Which of the following statements are true?


• Variance-increasing motifs were more frequent in unconserved regions such as active enhancers.

• Variance-increasing motifs were enriched in evolutionarily conserved regions such as gene promoters. 

• The authors found no difference between variance-increasing motifs and variance-decreasing motifs. 

• Trick question, all of the above are incorrect.

At what mean methylation level is variance highest?

• 0%

• 25%

• 50%

• 86.32%

• 100%

What is the purpose of the DNA module?

• To extract features from the DNA sequence

• To extract features from the CpG neighborhood of all cells

• To integrate evidence for predicting methylation states at target CpG sites

• To provide a baseline for holdout validation

What is the purpose of the CpG module?

• To extract features from the DNA sequence

• To extract features from the CpG neighborhood of all cells

• To integrate evidence for predicting methylation states at target CpG sites

• To provide a baseline for holdout validation

What is the purpose of the joint module?

• To extract features from the DNA sequence

• To extract features from the CpG neighborhood of all cells

• To integrate evidence for predicting methylation states at target CpG sites

• To provide a baseline for holdout validation

Which modules performed better than CpG Avg in genome wide testing? (select all that apply)

• DeepCpG

• DeepCpG CpG 

• WindowAvg

• RF Zhang

What steps were involved in the motif extraction process? (select all that apply)

• Averaging the activations for all input sequences.

• Averaging the dot product of weights/sequences for all inputs.

• Pearson correlation.

• Comparing learned motifs to the CIS-BP and ENCODE databases. 

Which of the following cell types were used? (select all that apply)

• HCC

• 2i

• EpiSC

• 2iSB

• mESC