Exam 4 for Bioinformatics for Biologists

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.

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, 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?

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?

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?

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?