Bioinformatics Exercises for 2nd year biomedical students 2017/2018

Part 1: Information Retrieval

The aim of this exercise is to get familiar with the use of available databases.
All the tools you will use are available online, you can follow the link from the exercise sheet or do a Google request to find them.
You will start with a genetic disorder and get more information about it.

Step 1: Finding the gene associated with a disease

What is Marfan syndrome? What are the phenotypic traits of Marfan syndrome?

What is the genetic cause of Marfan syndrome? Run a Google search.

Go to the OMIM database and search for Marfan syndrome. Do you find the same gene?

"OMIM, Online Mendelian Inheritance in Man, is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources."

QUESTIONS:

What is your disease associated gene?

Step 2: Get more information about your gene

OMIM and NCBI gene pages contain links to various databases.

Check the links in your OMIM gene page for more information.

What is the Ensembl Gene ID of your gene?
How many different transcripts are there for your gene according to Ensembl database, how many of them are translated?
In which tissue does your gene have a high expression? clue
What are the other diseases that your gene is associated with?

Check the links in your NCBI gene page for more information.

What is the Gene ID of your gene in NCBI database?
What is the RefSeq Gene ID of your gene?
What are the Gene Ontology terms associated with your gene?
What is the name of the mouse homolog of your gene? (try finding it starting from Ensembl or NCBI)
How many publications are there for the for your gene in human? In mouse?
Are there any invertebrate homologs?

Step 3: Visualization of your gene in a genome browser

Go to UCSC Genome Browser and find your gene. You can either go directly to UCSC or you can follow links from OMIM or NCBI gene pages.

How many exons does your gene have? (Don't count, find where it's written)
Look at the expression of your gene, does it correspond with your previous results?
What is the name of the 2 neighboring genes?
Open the conservation tracks, which parts of the gene show have high conservation? (You might need to zoom in to see clearly)

E06E4a | Bioinformatica