You have been assigned a GEO dataset (GPL570 expression profile for overexpression or knockdown/knockout study) to conduct your analyses. The assignment list is attached. Each student will work on the dataset assigned and perform GEO2R analysis between two groups and obtain gene list to analyze using databases.
MY DATASET: notch1 vs vector control Instructions are also shown below: 1) go to GEO dataset assigned to you to perform a GEO2R analysis between two groups. 2) Write down your hypothesis? (Hint: There is no difference between … and … conditions in terms of differential expression). 3) Identify the top 10 significantly upregulated genes and make a table indicating fold change, p value and adjusted p-value.
4) Identify the top 10 significantly downregulated genes and make a table indicating fold change, p value and adjusted p-value. 5) How much your gene that was overexpressed or knockdowned was affected by this experiment? If your gene is not present in the array please mention that. 6) Obtain 100-200 most upregulated and 100-200 most downregulated genes and separately analyze these gene lists using two of the databases you have learned in the class.
The aim is to identify how the overexpression or knockdown affects the transcriptome (HINT: annotation, networks, gene set enrichments, etc). Please explain your findings in your report. 7) Your report should be max. 1 page long in writing (except the figures/tables).