Applied Functional Genomics, 7.5 Credits

Contents

The course follows on from, and extends, the theoretical course Functional Genomics Theory, 7.5hp (5BI211). The course aims to provide an introduction to the application of modern techniques and analysis methods relevant to functional genomics. The course is project based and the students will gain practical insight and experience in how to perform analyses of large-scale datasets generated using either sequencing, proteomics or metabolomics methods. Groups of two to four work together to analyse data and produce a poster presentation of the results, which is presented at the end of the course. Students are responsible for their own time management but are provided with teaching support as needed.

Expected learning outcomes

After completing the course, students should be able to

1. Explain and understand how to extract and perform quality controls check for DNA, RNA, proteins and metabolites, including understanding why quality control is important and how to assess different aspects of quality.
2. Demonstrate, through application to the project analysis component of the course, understanding of the general principles of identifying differentially expressed genes, proteins or metabolites, including associated statistical issues and methods.
3. Demonstrate understanding of how to perform and visualise quality control checks of large-scale datasets by applications of these methods to the data analysed during the course
4. Produce figures that show understanding of the difficulties and solutions for the visualisation of large-scale data.
5. Show in-depth understanding of how the methods covered can be applied to address a functional genomics question
6. Present clear explanations of how and why methods of analysis were selected and applied to particular use case scenarios

Required Knowledge

90 ECTS credits including the course Functional Genomics Theory 7,5 ECTS credits. Swedish for basic eligibility for higher education programmes and English B/6. Requirements for Swedish only apply if the course is held in Swedish.

Form of instruction

The course is divided into two parts. At the start all students work together to learn techniques for sample preparation and quality control. The second part of the course involves working in groups of two to four students to perform analysis of either a genomics, proteomics or metabolomics dataset. Students will learn how to quality control check and analyse the data including identifying genes/proteins/metabolites of interest and how to obtain functional insight into their potential role. The analysis will include visualisation and statistical assessment. Students set their own working schedule for the group work but teachers are available when requested to offer guidance, advice and training.

Literature
Relevant literature is provided during the course, dependent in the specific details of the group project selected.
 

Examination modes

The course is examined by an online test graded G/U (ELO 1), a project work log graded VG, G, U (ELOs 2,5) and a final poster presentation. The poster session is graded VG, G, U (ELOs 2-6). Each group must prepare one poster to overview their project, including background, methods, results and discussion. Each member of the group will then individually present the poster to the course teachers and other students, including being asked questions about their work. The course leader will then assess the quality of the poster presentation. Grading will be assigned as VG, G or U. Grades: For engineering students; 5 Pass with distinction (G+2xVG), 4 Pass with merit 2xG, 1xVG), 3 Pass (3xG). For others; VG Pass with distinction (G+2xVG), G Pass (any other combination of VG+G), U Fail (U in any assessed component).
 
Students who fail are entitled to retake the failed examined component to obtain a passing grade in accordance with the Umeå University Regulations for tests and examinations at the undergraduate and graduate level (FS 1.1.2-553-14; HF 6 ch. 22 §). The time for re-examination happens in agreement with the course responsible teacher. Students who have passed an assessed component may not retake that component to obtain a higher grade. In cases where the examination cannot be repeated under the current rules for re-examination, the exam will be replaced with an alternative. The scope and content of such information should not be disproportionate to the missed examination. 
 
A student who has taken two examinations in a course, or part of a course, has the right to have another examiner. Requests for new-examiners should be addressed to the head of the Department of Plant Physiology.
 
In the event that the curriculum expires or major changes are made, a student is assured at least three examination opportunities (including the regular examination) based on the syllabus at taken by the student over a period of a maximum of two years from the date of the syllabus change.