Exam 4 Study Guide
There are project-based questions on Exam 4 that covers material from Units 12 through 15. There is no time limit for the exam. For the Exam, please be able to:
- Use Gene Expression Omnibus (GEO) to retrieve transcriptomics data and study information
- Identify differentially expressed genes
- Perform gene set enrichment analysis on transcriptomics data
- Visualize a network representation
- Report phenotype-gene relationships in OMIM
Exam questions are similar to homework questions.
Quiz Summary
0 of 6 Questions completed
Questions:
Information
You have already completed the quiz before. Hence you can not start it again.
Quiz is loading…
You must sign in or sign up to start the quiz.
You must first complete the following:
Results
Results
0 of 6 Questions answered correctly
Your time:
Time has elapsed
You have reached 0 of 0 point(s), (0)
Earned Point(s): 0 of 0, (0)
0 Essay(s) Pending (Possible Point(s): 0)
Categories
- Not categorized 0%
- 1
- 2
- 3
- 4
- 5
- 6
- Current
- Review
- Answered
- Correct
- Incorrect
-
Question 1 of 6
1. Question
Find the genome-wide analysis of gene expression in cancerous and normal human bladder tissues dataset (NCBI identifier: GSE52519) from NCBI’s Gene Expression Omnibus (GEO) and use it to answer the following questions:
-
Is GSE52519 published? If it is published, put the PMID number for the paper. Otherwise, type “None”.
What is the GEO identifier for the platform was used to profile samples for GSE52519?
Check the GEO provided information for one sample in GSE52519, specifically the “Data processing” section. Is GSE32861 data normalized? Yes or No.
CorrectIncorrect -
-
Question 2 of 6
2. Question
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. Use the DEG1 tab results to answer the following questions:
-
How many over-expressed (up) genes were identified?
How many under-expressed (down) genes were identified?
CorrectIncorrect -
-
Question 3 of 6
3. Question
Use the DEG2 tab results to answer the following questions:
-
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.
What is the most up-regulated pathway found from GO Biological Process?
What is the adjusted p-value for the most up-regulated pathway found from GO Biological Process?
CorrectIncorrect -
-
Question 4 of 6
4. Question
Use the Pathway tab results after you select the “GSEA (preranked fgsea)” method to answer the following questions:
-
What is the most down-regulated pathway found from GO Biological Process?
How many up-regulated pathways were found by GO Biological Process?
How many genes contributed to enrichment of the DNA conformation change pathway found from GO Biological Process?
CorrectIncorrect -
-
Question 5 of 6
5. Question
Use the Network tab results to answer the following questions:
-
A network of ____ genes was divided into ___ modules. , (2.5 points each)
How many genes are included in the blue module?
After selecting the blue module, list the 5 gene symbols shown in the network in alphabetical order. , , , , (1 point each)
After selecting the entire network, what was the most enriched pathway found from GO Biological Process?
CorrectIncorrect -
-
Question 6 of 6
6. Question
Using OMIM, answer the following questions:
-
How many gene/locus were identified with phenotype-gene relationships to bladder cancer. HINT: examine OMIM entry 109800.
Which gene/locus connected to bladder cancer is located at 11p15.5?
What is the gene symbol for the fibroblast growth factor receptor 3 gene connected to bladder cancer?
What type of mutation in these genes is connected to bladder cancer?
CorrectIncorrect -
