Plant Bioinformatics Capstone

University of Toronto via Coursera

Go to Course: https://www.coursera.org/learn/plant-bioinformatics-capstone

Introduction

**Course Review and Recommendation: Plant Bioinformatics Capstone on Coursera** In the dynamic field of plant biology, the Plant Bioinformatics Capstone course on Coursera stands out as a comprehensive and engaging learning experience. This course offers participants a unique opportunity to delve deep into the world of plant genomics, transcriptomics, and the broader implications of bioinformatics in understanding plant biology. ### Overview The Plant Bioinformatics Capstone is designed for learners who are eager to explore the advancements in plant biology that have emerged over the past 15 years. With the sequencing of countless plant genomes and the advent of RNA-seq methodologies, the course provides a solid foundation for understanding the variety of data available and how to harness it for research purposes. ### Syllabus Breakdown The course is meticulously structured, with a focus on practical application and hands-on learning. Each week builds on the last, encouraging learners to engage with real-world datasets and tools. 1. **Exploring Your Gene of Interest**: In the first week, students embark on an exploration of a gene from Arabidopsis, specifically At3g20300. Utilizing various online databases, participants will gather valuable information about the gene, including its size, homologs, phylogenetic relationships, and expression patterns. This early focus on data acquisition highlights the course’s emphasis on critical thinking and analysis. 2. **Identifying Related Genes**: Building on the previous week, the second module introduces students to the concept of coexpression analyses. By examining the genes coexpressed with At3g20300, learners gain insights into potential functionalities based on the relationships and common regulatory motifs shared among these genes. This approach underscores the interplay between genetic networks and their implications for biological pathways. 3. **Gene Function and Network Analysis**: The third week delves into gene ontology enrichment analysis, equipping students with the skills to infer functionalities for their target gene based on the behaviors of coexpressed genes. Students will also learn to apply network tools to discover additional linkages, enhancing their understanding of gene interactions and networks — a critical aspect of bioinformatics. 4. **Drafting and Finalizing the Lab Report**: The final weeks of the course are dedicated to synthesizing the research findings into a cohesive lab report. Students will learn the importance of literature reviews, proposing experiments, and receiving feedback through peer reviews. The capstone project culminates in presenting a polished report that encapsulates their learning journey and discoveries about the function of their chosen gene. ### Course Highlights - **Hands-On Learning**: The course leverages online databases effectively, giving students the skills needed to navigate and utilize bioinformatics tools. - **Research-Oriented Approach**: With a focus on current literature and methodologies, students are prepared for real-world challenges in plant biology. - **Collaboration and Feedback**: The peer-review component fosters a collaborative learning environment, encouraging students to refine their ideas and engage critically with peer work. - **Comprehensive Assessment**: The final report not only serves as an examination of acquired knowledge but also as a portfolio piece for future academic or professional pursuits. ### Recommendation For anyone interested in the intersection of plant biology and bioinformatics, the Plant Bioinformatics Capstone course on Coursera is highly recommended. It’s suitable for those who have some foundational knowledge in biology and coding, as well as those who are looking to deepen their understanding in plant genetics. The course offers a rich learning experience that prepares participants for advanced research, equipping them with essential skills to analyze and interpret genomic data. Overall, this course is an excellent way for aspiring biologists, bioinformaticians, and researchers to bolster their resumes and build a solid expertise in an increasingly essential field of study.

Syllabus

Exploring your gene of interest with online databases

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.

Identifying genes related to your gene of interest

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.

Analysis of the function of your gene of interest and its network of genes

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.

Lab report draft

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.

Final copy of lab report

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).