Hypothetical Protein Annotation Homework 10

The following analysis uses a gene expression dataset of nitrogen deficient and nitrogen sufficient root and shoot tissues from Oryza sativa under phosphorous deficient conditions acquired from NCBI’s Gene Expression Omnibus (NCBI identifier: GSE73775). To save time, the relevant information from the series matrix and the platform files have been provided in the attached text files. Use the 2 GSE73775 files as input to iDEP and collect the results from the “Gene lists” and “FDR & fold-changes for all genes” files downloadable from the DEG1 tab. You will use the “FDR & fold-changes for all genes” files in later homework. For this homework, open each Gene list and the provided platform file in Excel and compare the Gene list to the platform file using “Conditional Formatting” to identify duplicates. Next, use “Custom Sort” by cell color to separate duplicates from non-duplicates for removal. Another “Sort by smallest to largest” for the Description column using just duplicates will make it easier to find hypothetical proteins. Save these results for future use, then answer the following questions