Use of Biological Pathway Databases, Primarily Open Source
June 4, 2015
12:00 Noon ET
Presenter: Marc Gillespie, St. John’s University, Jamaica, New York
We encourage anyone interested in the use of bioinformatics databases to participate in the next Undergraduate Educator Network Webinar.
Sifting through the results of expression or other data rich analyses poses a daunting challenge to experienced and new researchers alike. Numerous methods exist, all sharing the common theme of grouping the results in such a way as to assist the researcher in finding the underlying patterns in the data. Biological pathway knowledge bases provide a platform for the identification of pathways that are represented within the experimental data.
Within the classroom, pathway knowledge bases can function as a biology textbook. Faculty and Students can select specific pathways that impact a segment of their material and highlight the biological mechanisms that are in play within this segment. Imagine a classroom presentation describing DNA damage that highlights the molecular steps of DNA Repair. Students can walk themselves through each type of DNA Repair, examining the differences between mismatch and base excision repair mechanisms. Students and Faculty examining the steps are immediately connected to the literature describing the experiments that support each step of the pathway, molecular structure data, and expression data. Each step of the pathway includes a text summation, as well as possible links to relevant disease states affecting that particular step.
Webinar Objectives and Educational Goals
1. Analyze expression datasets and other data rich experimental results.
a. Faculty and Students can use topic specific datasets to highlight molecular function and functional interconnections.
2. Describe the methods that are used for biological pathway analysis.
a. Multiple methods are available. What are they, how are they used?
b. How might some of these methods be integrated into a class, or independent assignment activity to introduce or reinforce classroom topics?
3. Identify pathways that are over-represented within experimental data sets.
a. What is pathway over-representation? What are the p values assigned to these matches telling me?
b. What can I learn from this analysis?
4. Use Reactome, an open-source, open access, manually curated and peer-reviewed pathway knowledgebase.
a. Practicing all of these objectives within the Reactome framework.
5. Describe ID mapping, pathway assignment, and over-representation analysis and include these analysis as modules within a classroom setting.
a. Best practices for summarizing pathway data analysis for Students and Faculty.
b. Common pitfalls
Missed a previous UEN Webinar
The Undergraduate Education Subcommittee has facilitated the development of a library of webinars related to the instruction of undergraduate toxicology. Recordings and slides are available at Undergraduate Education Network Webinars.
Past titles include:
- Having It All: Teaching, Research, and Service at a Small Liberal Arts College: A Toxicologist's Perspective
- Education and Enrichment Activities for Educators
- The Use of Technology to Teach Toxicology and Related Disciplines
- Evidence-Based Instructional Practices in Undergraduate Science Courses
- Academic Service Learning (AS-L) in an Undergraduate Pharmacology Course
Have an idea for new Webinars?
If you have an idea for future UEN webinars, we are soliciting new ideas now. Please contact Kristine Willett with any suggestions of topics that would be useful to undergraduate toxicology educators.