Exam 4 for Bioinformatics for Biologists

Is GSE52519 published? If it is published, put the PMID number for the paper. Otherwise, type “None”. Fill in the blank 1 of 3
What is the GEO identifier for the platform was used to profile samples for GSE52519? Fill in the blank 2 of 3
Check the GEO provided information for one sample in GSE52519, specifically the “Data processing” section. Is GSE32861 data normalized? Yes or No. Fill in the blank 3 of 3

How many over-expressed (up) genes were identified? Fill in the blank 1 of 2
How many under-expressed (down) genes were identified? Fill in the blank 2 of 2

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? Fill in the blank 1 of 4
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. Fill in the blank 2 of 4
What is the most up-regulated pathway found from GO Biological Process? Fill in the blank 3 of 4
What is the adjusted p-value for the most up-regulated pathway found from GO Biological Process? Fill in the blank 4 of 4

What is the most down-regulated pathway found from GO Biological Process? Fill in the blank 1 of 3
How many up-regulated pathways were found by GO Biological Process? Fill in the blank 2 of 3
How many genes contributed to enrichment of the DNA conformation change pathway found from GO Biological Process? Fill in the blank 3 of 3

A network of ____ genes was divided into ___ modules. Fill in the blank 1 of 9 , Fill in the blank 2 of 9 (2.5 points each)
How many genes are included in the blue module? Fill in the blank 3 of 9
After selecting the blue module, list the 5 gene symbols shown in the network in alphabetical order. Fill in the blank 4 of 9 , Fill in the blank 5 of 9 , Fill in the blank 6 of 9 , Fill in the blank 7 of 9 , Fill in the blank 8 of 9 (1 point each)
After selecting the entire network, what was the most enriched pathway found from GO Biological Process? Fill in the blank 9 of 9

How many gene/locus were identified with phenotype-gene relationships to bladder cancer. HINT: examine OMIM entry 109800. Fill in the blank 1 of 4
Which gene/locus connected to bladder cancer is located at 11p15.5? Fill in the blank 2 of 4
What is the gene symbol for the fibroblast growth factor receptor 3 gene connected to bladder cancer? Fill in the blank 3 of 4
What type of mutation in these genes is connected to bladder cancer? Fill in the blank 4 of 4