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Exercise session 1

Exercise session 1. Exercise 1 OMIM: identify disease related genes. Tasks: choose a gene and identify terms that characterize it. some examples: Alzheimer, breast cancer What human genes are related to hypertension?

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Exercise session 1

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  1. Exercise session 1

  2. Exercise 1OMIM: identify disease related genes Tasks: • choose a gene and identify terms that characterize it. some examples: Alzheimer, breast cancer • What human genes are related to hypertension? • Retrieve the OMIM record for the cystic fibrosis transmembrane conductance regulator (CFTR), and link to related protein sequence records in Entrez. • Find the OMIM record for the p53 tumor protein, and linkout to related information in Entrez Gene and the p53 Mutation Database.

  3. Exercise 1

  4. Exercise 1GO: identify genes and concepts Tasks: • Use [Gene Ontology] and try to identify one or more relevant terms to describe a specific gene. • Use the selected term(s) to find the gene in [Entrez Gene]. Be aware of the species you select when querying Entrez Gene. • Describe the information found in the record of your selected gene. • See if there are additional links to other resources like KEGG Pathways, UniGENE, ... • What kind of information is stored under these additional links?

  5. Exercise 1Sequence Level Tasks: • Select a Genbank sequence from the Entrez Gene record of your gene. • What kind of information is stored in the Genbank record? • Save the protein sequence of your gene in fasta format. Use the display and send to file buttons. • Select a set of protein sequences related to your gene. • Save a selection five to ten protein neighbours in one fasta file.

  6. Exercise 1Sequence Level Tasks: • Locate the gene in the complete human genome. Use the Ensembl genome browser. • Use the accession number of your gene to find the info on Ensembl. • Where is your gene located on the genome? • Are there any alternative transcripts or orthologues found? • How is this information found (homology, prediction, ESTs) and is there any information according its reliability?

  7. Exercise 1Sequence Level Tasks: • With BLAST you can identify homologous sequences of your gene in the huge genome database. • Do a blastn with the saved DNA sequence. • Do a blastp with the saved protein sequence • How well do these results match? What are the differences if there are any? • Do the hits retrieved with blastp correspond to the neighbouring proteins you saved before?

  8. Exercise 1Sequence Level Tasks: • To functionally annotate a given protein, we can use several prediction tools. A large collection of tools is available at [Expasy]. • Start with the ScanProsite tool to find specific domains in your protein sequence. • Are there any relevant features found? • Try the MotifScan and InterProScan tools. • What kind of feature are predicted and how do the different tools correspond to each other? • How do the predictions correspond to the annotations in Ensembl?

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