//localhost:4321/key-objective-2/agatashakira-the-aop-project-part-9/index.html The AOP project ► Key objective 2 Author: Shakira Agata This Jupyter Notebook shows the steps for the execution of KE enrichment analysis and benchmarking to Overrepresentation Analysis(ORA) for dataset:E-GEOD-69851. This notebook is subdivided into fourteen sections: Section 1: Creation of dictKE dictionary Section 2: Creation of dictWP dictionary Section 3: Creation of KEgenes dictionary Section 4: Calculation of N variable Section 5: Comparison 1: Bisphenol A 100uM Section 5.1: Calculation of n variable Section 5.2: Calculation of variable B and variable b Section 5.3: Calculation of enrichment score & hypergeometric p-value Section 5.4: Filtering results Section 5.5: Calculation of percent gene overlap Section 5.5.1 Creation of significant KE table Section 5.5.2 Significant ORA pathway table Section 5.5.3 Creation of for loop Section 5.5.4 Tabulation Section 5.5.5 Percent overlap calculation Section 6: Comparison 2: Bisphenol A 1uM Section 6.1: Calculation of n variable Section 6.2:Calculation of variable B and variable b Section 6.3: Calculation of enrichment score & hypergeometric p-value Section 6.4: Filtering results Section 6.5: Calculation of percent gene overlap Section 6.5.1 Creation of significant KE table Section 6.5.2 Significant ORA pathway table Section 6.5.3 Creation of for loop Section 6.5.4 Tabulation Section 6.5.5 Percent overlap calculation Section 7: Comparison 3: Farnesol 100uM Section 7.1: Calculation of n variable Section 7.2:Calculation of variable B and variable b Section 7.3: Calculation of enrichment score & hypergeometric p-value Section 7.4: Filtering results Section 7.5: Calculation of percent gene overlap Section 7.5.1 Creation of significant KE table Section 7.5.2 Significant ORA pathway table Section 7.5.3 Creation of for loop Section 7.5.4 Tabulation Section 7.5.5 Percent overlap calculation Section 8: Comparison 4: Tetrachlorodibenzo dioxin 100nM Section 8.1: Calculation of n variable Section 8.2:Calculation of variable B and variable b Section 8.3: Calculation of enrichment score & hypergeometric p-value Section 8.4: Filtering results Section 8.5: Calculation of percent gene overlap Section 8.5.1 Creation of significant KE table Section 8.5.2 Significant ORA pathway table Section 8.5.3 Creation of for loop Section 8.5.4 Tabulation Section 8.5.5 Percent overlap calculation Section 9: Comparison 5: Tetrachlorodibenzo dioxin 1nM Section 9.1: Calculation of n variable Section 9.2:Calculation of variable B and variable b Section 9.3: Calculation of enrichment score & hypergeometric p-value Section 9.4: Filtering results Section 9.5: Calculation of percent gene overlap Section 9.5.1 Creation of significant KE table Section 9.5.2 Significant ORA pathway table Section 9.5.3 Creation of for loop Section 9.5.4 Tabulation Section 9.5.5 Percent overlap calculation Section 10: Comparison 6: Troglitazone 100uM Section 10.1: Calculation of n variable Section 10.2:Calculation of variable B and variable b Section 10.3: Calculation of enrichment score & hypergeometric p-value Section 10.4: Filtering results Section 10.5: Calculation of percent gene overlap Section 10.5.1 Creation of significant KE table Section 10.5.2 Significant ORA pathway table Section 10.5.3 Creation of for loop Section 10.5.4 Tabulation Section 10.5.5 Percent overlap calculation Section 11: Comparison 7: Troglitazone 10uM Section 11.1: Calculation of n variable Section 11.2: Calculation of variable B and variable b Section 11.3: Calculation of enrichment score & hypergeometric p-value Section 11.4: Filtering results Section 11.5: Calculation of percent gene overlap Section 11.5.1 Creation of significant KE table Section 11.5.2 Significant ORA pathway table Section 11.5.3 Creation of for loop Section 11.5.4 Tabulation Section 11.5.5 Percent overlap calculation Section 12: Comparison 8: Troglitazone 1uM Section 12.1: Calculation of n variable Section 12.2: Calculation of variable B and variable b Section 12.3: Calculation of enrichment score & hypergeometric p-value Section 12.4: Filtering results Section 12.5: Calculation of percent gene overlap Section 12.5.1 Creation of significant KE table Section 12.5.2 Significant ORA pathway table Section 12.5.3 Creation of for loop Section 12.5.4 Tabulation Section 12.5.5 Percent overlap calculation Section 13: Comparison 9: Valproic acid 1mM Section 13.1: Calculation of n variable Section 13.2:Calculation of variable B and variable b Section 13.3: Calculation of enrichment score & hypergeometric p-value Section 13.4: Filtering results Section 13.5: Calculation of percent gene overlap Section 13.5.1 Creation of significant KE table Section 13.5.2 Significant ORA pathway table Section 13.5.3 Creation of for loop Section 13.5.4 Tabulation Section 13.5.5 Percent overlap calculation Section 14: Metadata Section 1: Creation of dictKE dictionary In this section, the dictKE dictionary will be made which is used to retrieve the first neighbors of the key events present in the inflammatory stress response pathway AOP network. 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