BIO4211 Genomics, Transcriptomics and Proteomics, 4 ECTS

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BIO4211 Genomics, Transcriptomics and Proteomics 4 ECTS

Course homepage

Organised by

Master's Degree Programme in Bioinformatics

Person in charge

Martti Tolvanen

Preceding studies

Alternatively BIKE2080

Belongs to following study modules

Keywords

Strategic themes: Internationalisation

General description

This course facilitates the conceptual transition from individual genes and proteins to full datasets of genomes, transcriptomes and proteomes. In addition, you learn how to utilize large datasets for extracting information of individual genes and proteins.

Learning outcomes

Familiarity with Internet sources for genome-wide data; basic skills in using tools at these web sites; understanding how modern high-throughput methods generate sequence data and gene and protein expression data; practical skill of using genome browsers to access genome data and genome comparison data; understanding gene prediction and genome annotation pipelines; skill of perfoming individual gene predictions; understanding different levels of variation in human genomes; understanding basic workflows of microarray data analysis and next-generation sequencing data analysis; basic knowledge of experimental methods in proteomics and metabolomics which enables understanding data analysis in these fields; skill of identifying proteins from mass spectroscopic data.

Next-generation sequencing (NGS); Ensembl genome browser and its comparative genomics tools; gene variations and variation databases; metagenomics; transcript expression data from microarrays and NGS, and principles of their analysis; finding over- and under-expressed genes from expression data; clustering of data; concept of functional enrichment; proteomics of protein expression, interactions and structures; and metabolic networks and metabolomics data.

Teaching methods

Teaching method	Contact	Online
Independent work	0 h	80 h

The course can be started at any time, with a deadline of 12 weeks after starting.

Teaching language

English

Modes of study

Option 1

Available for:

Degree Programme Students
Other Students
Open University Students
Doctoral Students
Exchange Students

In learning diary Exercise(s)

In English

In learning diary Essay

In English

Evaluation

Numeric 1-5.

Your learning diary is counted towards 80% of the total score. The diary will contain a mix of summaries, essays, discussion, and exercises/mini projects. For the highest grades, your diary should contain an element of reflectiveness (description of your learning process, what you consider to be the important things learned in each study session, questions you put to yourself); tackling many practical problems; and finding additional sources to support your learning.

Web & Moodle Participation in course work

In English

Evaluation

Your Moodle activity counts towards 20% of the total score. For "points" of Moodle activity, you can either start relevant discussions in the Moodle forums (for example, by sharing reports of analyses or mini projects you have completed), contribute meaningful comments/answers in a discussion, provide suggestions for new topics or resources for the course pages, or report new links to replace outdated ones.

In addition to your reflection and summaries, the learning diary will contain exercises and assignments, which will be chosen individually, to be discussed with your tutor. Your learning diary can be written in Finnish if agreed with the web tutor.

Evaluation and evaluation criteria

Numeric 1-5.
Your learning will be evaluated based on your learning diary work and Moodle activity. Evaluation criteria include demonstrating the understanding of key concepts in your diary text, completing exercises successfully, reflection of your learning, sharing of your ideas and findings in the forums, and working in the given 12-week deadline.