Homework 12: Fill in the blank – 2 points each entry – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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1. Question
Find 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) and use it to answer the following questions:
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What is the experiment type for data provided in GSE32861?
Is GSE32861 published? If it is published, put the PMID number for the paper. Otherwise, type “None”.
Data is provided for ____ lung adenocarcinoma and ____ matched adjacent non-tumor lung tissue.
What is the name of the platform was used to profile samples for GSE32861?
What is the GEO identifier for the platform was used to profile samples for GSE32861?
Check the GEO provided information for one sample in GSE32861, specifically the “Data processing” section. Is GSE32861 data normalized? Yes or No.
Download the series matrix file for GSE32861 and decompress (i.e., unzip) it. Download the full data table for the platform used to profile GSE32861 samples. Open both text files in Excel to answer the following questions:
What is the total number of data rows provided in the series matrix file?
What is the number for the first row containing probe data?
What column in the platform file contains Entrez Gene ID values for probes?
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 results to answer the following questions:
How many over-expressed (up) genes were identified?
How many under-expressed (down) genes were identified?
By examining the “Gene list & data” file from DEG2, were all probes successfully converted to Ensembl IDs? Yes or No.
By examining the “Gene list & data” file from DEG2, what is the gene symbol for the most over-expressed (up) gene identified by log2 Fold Change?
By examining the “Gene list & data” file from DEG2, what is the log2 Fold change value for the most under-expressed (down) gene identified? Round your answer to 2 decimal places.
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