Homework 13: Fill in the blank – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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This exercise is a continuation of analysis on the gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue dataset (NCBI identifier: GSE32863) from NCBI’s Gene Expression Omnibus (GEO). To save time, the relevant information from the series matrix file and the platform file have been combined and provided in the attached text file. Use this file as input to iDEP and use the DEG2 tab results to answer the following questions:
What is the most down-regulated pathway found from GO Biological Process?
What is the adjusted p-value for the most up-regulated pathway found from GO Biological Process? (4 points)
How many up-regulated pathways were found by GO Biological Process?
How many down-regulated pathways were found by GO Biological Process?How many genes contributed to enrichment of the most down‑regulated pathway found from KEGG?
How many up-regulated pathways were found by KEGG?
Were the same down-regulated pathways found between GO Biological Process and KEGG? Yes or No.Use the Pathway tab results after you select the “GSEA (preranked fgsea)” method to answer the following questions:
Was the most down-regulated pathway found from GO Biological Process on the DEG2 tab listed among the most down-regulated pathway found from GO Biological Process on the Pathway tab? Yes or No.
Was the most down-regulated pathway found from GO Biological Process on the Pathway tab listed among the most down-regulated pathway found from GO Biological Process on the DEG2 tab? Yes or No.
What is the most down-regulated pathway found from GO Biological Process?
What is the most up-regulated pathway found from GO Biological Process?
How many down-regulated pathways were found by GO Biological Process?
How many up-regulated pathways were found by GO Biological Process?
How many genes contributed to enrichment of the keratinization pathway found from GO Biological Process?
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