University of Toronto

Plant Bioinformatics Capstone

This course is part of Plant Bioinformatic Methods Specialization

Taught in English

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4,158 already enrolled

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Course

Gain insight into a topic and learn the fundamentals

4.6

(28 reviews)

Intermediate level
Some related experience required
9 hours (approximately)
Flexible schedule
Learn at your own pace

Details to know

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Assessments

3 quizzes

Course

Gain insight into a topic and learn the fundamentals

4.6

(28 reviews)

Intermediate level
Some related experience required
9 hours (approximately)
Flexible schedule
Learn at your own pace

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This course is part of the Plant Bioinformatic Methods Specialization
When you enroll in this course, you'll also be enrolled in this Specialization.
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There are 5 modules in this course

In the Week 1 module, we are going to use an example gene of (mostly) unknown function from Arabidopsis, At3g20300, and see what online databases can tell us about that gene. Part A uses tools that we have explored in Plant Bioinformatics to gather information about the gene/gene product, such as its size, what its homologs are, phylogenetic relationship to other sequences, domain information, and subcellular localization. Part B explores gene expression databases to see where that gene is expressed. Often where and when a gene is expressed can give us clues as to its function.

What's included

2 readings1 quiz

Often the function of genes that are coexpressed with a gene of unknown function can give us hints about the function of that gene. Researchers are now often using coexpression analyses as “primary screens” to identify “new” genes in biological pathways (a few examples are described in Usadel et al., 2009). Another interesting facet is whether the promoters of these sets of coexpressed genes contain any common cis-regulatory motifs. In Part A, we’ll explore the genes that are coexpressed with At3g20300, and in Part B, we’ll look for common regulatory motifs.

What's included

2 readings1 quiz

Gene Ontology enrichment analysis for a set of coexpressed gene is often useful for figuring out what that group of genes is doing. By doing such analyses with a set of coexpressed genes can we infer a role for our gene of unknown function? We'll explore this aspect in Part A, along with investigating potential pathways the gene list is involved in. In Part B, we'll use other network tools to investigate additional linkages to other genes, above and beyond those suggested by coexpression. It is sometimes useful to investigate these too! Again, we'll be using At3g20300 as our example.

What's included

2 readings1 quiz

Now we will take the above analyses and synthesize the information from them into a draft lab report/essay describing the putative function of our gene of interest with unknown function. We'll draw on the literature to describe what is known about related genes, and propose some experiments to test our hypotheses about our gene's potential function.

What's included

2 readings1 peer review

Based on feedback from peer reviews, we'll polish our draft to submit a final report! The report should be around 13-15 pages long (double spaced) including figures, which should be included inline. The page count does not include Methods or References (see Example Essay for format).

What's included

1 peer review

Instructor

Instructor ratings
4.5 (6 ratings)
Nicholas James Provart
University of Toronto
5 Courses122,871 learners

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4.6

28 reviews

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5

Reviewed on Jun 22, 2020

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4

Reviewed on Jun 5, 2023

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