Enrichment Analysis June 27, 2024 Enrichment Analysis Name* 1. On the GSEA website’s Molecular Signatures Database (MSigDB) within human collections, how many C2: curated gene sets are available? 50 301 7,233 16,008 2. Among the 227 gene-set libraries provided by Enrichr, which library has the widest range of gene coverage? ChEA_2022 LINCS_L1000_Chem_Pert_up Epigenomics_Roadmap_HM_ChIP-seq Enrichr_Users_Contributed_Lists_2020 3. When performing enrichment analysis by clicking on the “breast cancer” button on the Enrichr interface, while keeping all the default settings, when looking at the ARCHS4 TFs co-expression results, which transcription factor has the lowest p-value? Note: Gene symbols will be added by Enrichr to the input box in a few seconds after you click on the breast cancer button. ATF3 HIF1A NFE2L2 TFAP2A 4. Choose the term that best fits the analysis performed. Dimensionality reduction Differential expression analysis Clustering analysis Enrichment analysis 5. Which resources can be used as a source for creating gene set libraries? A and B A and D B and C All of them 6. Which statement is most true about the p-value when performing enrichment analysis with the Fisher Exact test for Pathway A and the input gene set assuming a background of 20,000 genes? P < 0.0001 P < 0.001 P < 0.01 All statements are true 7. Select the incorrect explanation about the peak highlighted in the red circle. Gaussian running sum Enrichment score Maximum displacement from zero The largest deviation from the baseline 8. Which is the correct statement about the formula below in Gene Set Enrichment Analysis (GSEA)? It is the amount to increment the walk when the gene is in the set It is the amount to decrement the walk when the gene is in the set It is the wrong formula, G should be replaced by N It is the amount to increment the walk when the gene is NOT in the set 9. Select the most relevant shape of the distribution graph that the displacement in a random walk typically follows. A B C D 10. You are standing in front of Mount Sinai on Madison Avenue. You have a quarter coin in your hand that you can toss. Every time when tossing the coin you take one step north (towards Harlem) if you get “heads” from the toss, or if you get “tail” you make a step south (towards Midtown). Each step that you take is about one foot. What is your most likely position after taking 10,000 tosses/steps? It is not possible to guess 100 feet toward Midtown 100 feet toward Harlem Still be at the same spot in front of Mount Sinai Submit