Week 7 - Ontologies & Functional Enrichment Analysis
This week we will be learning about ontologies. These structured resources allow us to used semantically meaningful restricted vocabularies to annotate biological data and enable rigorous computational analysis. Ontologies are key to imposing structure on the largely unstructured data we deal with as Bioinformaticians. By using standardised concepts to describe things we enable key essential features of quantitative research and inter-operability.
We will also be learning about ways that we can use ontologies and annotation in two different quantitative approaches to gain insight from the lists of genes and proteins that are often produced by laboratory experiments.
Lecture 7 - Ontologies & Functional Enrichment Analysis
The lecture slides for Week 7 - "Ontologies & Functional Enrichment Analysis" are available here.
The video of the lecture will be available from the GitHub video area here.
Reading Lists & Resources
Each week we will have an accompanying reading list with some articles & web-sites for self study to support the course. You can find the course "Resource List" - here. We will continue to curate the list throughout the course especially if things pop up in the lectures and practicals that we want to add a reference or link to so do please check back in on the list from time to time.
We have generally tried to identify resources as "Essential", "Recommended" or "Further Reading" in an attempt to help you prioritise your reading during the course.
Finally a very important time to draw your attention to what you can consider the "core text" for the course, which is the excellent "Bioinformatics & Functional Genomics" Third Edition by Jonathan Pevsner. You will be pleased to know that this text-book is available free online as part of the University's subscription portfolio. You can find it right at the top of the resource list. If you have any problems accessing or using any of the above please do drop us a comment in the Discussion forum and we will try to get things resolved as soon as possible.
This week we have two journal articles for you to read, which are on the resource list, but here also for convenience:
- Aleksander, Suzi A., Seth Carbon, J. Michael Cherry, Harold J. Drabkin, Marc Feuermann, Pascale Gaudet, et al. 2023. “The Gene Ontology Knowledgebase in 2023” edited by A. Baryshnikova. Genetics (Austin) 224(1). doi: 10.1093/genetics/iyad031.
- Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. 2005. “Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles.” Proceedings of the National Academy of Sciences - PNAS 102(43):15545–50. doi: 10.1073/pnas.0506580102.