Plant Bioinformatics Capstone from Coursera

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse or tap of a finger.

In Plant Bioinformatics on Coursera.org, we covered 33 plant-specific online tools from genome browsers to transcriptomic data mining to promoter/network analyses and others, and in this Plant Bioinformatics Capstone we'll use these tools to hypothesize a biological role for a gene of unknown function, summarized in a written lab report.

This course is part of a Plant Bioinformatics Specialization on Coursera, which introduces core bioinformatic competencies and resources, such as NCBI's Genbank, Blast, multiple sequence alignments, phylogenetics in Bioinformatic Methods I, followed by protein-protein interactions, structural bioinformatics and RNA-seq analysis in Bioinformatic Methods II, in addition to the plant-specific concepts and tools introduced in Plant Bioinformatics and the Plant Bioinformatics Capstone.

This course/capstone was developed with funding from the University of Toronto's Faculty of Arts and Science Open Course Initiative Fund (OCIF) and was implemented by Eddi Esteban, Will Heikoop and Nicholas Provart. Asher Pasha programmed a gene ID randomizer.

What's inside

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).

Good to know

Know what's good

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Specializes in Bioinformatics and Plant Biology, providing insightful knowledge for those interested in these fields

Delves into cutting-edge techniques and tools, preparing learners for current industry practices

Builds on foundational concepts in Bioinformatics, suitable for learners with prior knowledge or who have completed the prerequisite course

Involves hands-on exercises, allowing learners to apply concepts and gain practical experience

Provides opportunities to explore real-world datasets and analyze biological problems

Facilitated by recognized experts in Plant Bioinformatics, ensuring high-quality instruction

Reviews summary

Capstone in plant bioinformatics

learners say this engaging course provides a great experience in plant bioinformatics, especially for professionals seeking to advance their genomics studies. They praise the resources, assignments, and instructor.

Course has engaging assignments focusing on real world problems

"compels you to use all the possible plant databases and tools available online to assign the function to an unknown gene sequence."

"A challenging course unlike the first three"

Course provides strong resources for learning plant bioinformatics

"provided me with more information about other plant databases apart from NCBI"

"Excellent bioinformatic training and experience."

Instructor is wonderful and responsive

"Nick is a wonderful mentor who takes time everyday to answer our every query."

"Excellent bioinformatic training and experience."

Course is difficult and geared toward more experienced learners

"this last one is just for professionals."

"to complete this last one, I guess we need to be at least doing our master degree."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Plant Bioinformatics Capstone with these activities:

Mentor other students in bioinformatics

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Help your peers learn about bioinformatics.

Browse courses on Mentoring

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Find a student who needs help with bioinformatics.
Meet with the student to help them with their work.
Answer the student's questions.

Review basic biology concepts

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Refresh your knowledge of basic biology concepts.

Browse courses on Biology

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Review your notes from high school or college biology courses.
Take a practice quiz on basic biology concepts.

Tutorial on using CLC Workbench

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Become familiar with the CLC Workbench, a powerful tool for sequence analysis.

Browse courses on Sequence Analysis

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Watch the CLC Workbench tutorial.
Use the CLC Workbench to assemble and analyze a sequence.

Five other activities

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Practice promoter analysis

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Practice your promoter analysis skills by using online tools to analyze the promoters of genes of interest.

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Choose a gene of interest.
Use an online promoter analysis tool to identify potential regulatory elements in the promoter.
Predict the expression pattern of the gene based on the identified regulatory elements.

Read An Introduction to Bioinformatics Algorithms

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Gain a deeper understanding of the algorithms used in bioinformatics.

View An Introduction to Bioinformatics Algorithms on Amazon

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Read the book
Solve the exercises

Participate in a bioinformatics competition

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Test your bioinformatics skills against other students.

Browse courses on Bioinformatics

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Find a bioinformatics competition to participate in.
Register for the competition.
Solve the problems in the competition.

Create a gene expression database

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Build your own gene expression database to store and analyze gene expression data.

Browse courses on Gene Expression

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Use a database management system to create a database.
Design a schema for the database.
Import gene expression data into the database.
Create a user interface to access the database.

Build a gene regulatory network

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Build a gene regulatory network to predict gene expression.

Browse courses on Network Analysis

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Collect gene expression data.
Identify transcription factors.
Build a network of transcription factors and their target genes.
Use the network to predict gene expression.

Career center

Learners who complete Plant Bioinformatics Capstone will develop knowledge and skills that may be useful to these careers:

Bioinformatics Scientist

A Bioinformatics Scientist uses computer science and mathematics to analyze and interpret biological data. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Bioinformatics Scientist, particularly for those working on plant-related projects, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Bioinformatics Scientist

Computational Biologist

A Computational Biologist uses computer science and mathematics to analyze and interpret biological data. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Computational Biologist, particularly for those working on plant-related projects, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Computational Biologist

Biostatistician

A Biostatistician designs and analyzes experiments, collects and interprets data, and develops statistical models to solve problems in the life sciences. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. This may be useful for a Biostatistician, particularly for those working on plant-related projects, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Biostatistician

Research Scientist

A Research Scientist conducts scientific research to advance knowledge and develop new technologies. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Research Scientist working on plant-related research, as the course uses many plant-specific databases and tools.

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Geneticist

A Geneticist studies genes and heredity. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including genetic data. As such, this course may be useful for a Geneticist, particularly for those working on plant genetics, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Geneticist

Systems Biologist

A Systems Biologist studies the interactions between different components of a biological system. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Systems Biologist working on plant-related systems, as the course uses many plant-specific databases and tools.

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Plant Pathologist

A Plant Pathologist studies the causes and effects of plant diseases. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including data on plant pathogens. As such, this course may be useful for a Plant Pathologist, particularly for those working on developing new methods for controlling plant diseases.

See salaries and explore the career path for Plant Pathologist

Molecular Biologist

A Molecular Biologist studies the structure and function of molecules in living organisms. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including molecular data. As such, this course may be useful for a Molecular Biologist, particularly for those working on plant molecular biology, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Molecular Biologist

Plant Scientist

A Plant Scientist studies plants and their growth, development, and uses. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including data on plants. As such, this course may be useful for a Plant Scientist, particularly for those working on developing new methods for improving plant growth and yield.

See salaries and explore the career path for Plant Scientist

Plant Breeder

A Plant Breeder develops new plant varieties by crossing and selecting plants with desirable traits. This course introduces bioinformatics resources and techniques that can be used to analyze plant data. As such, this course may be useful for a Plant Breeder, particularly for those working on developing new plant varieties with improved traits.

See salaries and explore the career path for Plant Breeder

Plant Geneticist

A Plant Geneticist studies the genes and heredity of plants. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including genetic data. As such, this course may be useful for a Plant Geneticist, particularly for those working on plant genetics, as the course uses many plant-specific databases and tools.

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Data Scientist

A Data Scientist uses mathematics and computer science to analyze and interpret data. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Data Scientist working on plant-related data, as the course uses many plant-specific databases and tools.

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Plant Physiologist

A Plant Physiologist studies the physical and chemical processes that occur in plants. This course introduces bioinformatics resources and techniques that can be used to analyze biological data, including data on plant physiology. As such, this course may be useful for a Plant Physiologist, particularly for those working on developing new methods for improving plant growth and yield.

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Data Analyst

A Data Analyst collects, processes, and analyzes data to extract meaningful insights. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Data Analyst working on plant-related data, as the course uses many plant-specific databases and tools.

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Database Administrator

A Database Administrator designs, implements, and maintains databases. This course introduces bioinformatics resources and techniques that can be used to analyze biological data. As such, this course may be useful for a Database Administrator working on plant-related databases, as the course uses many plant-specific databases and tools.

See salaries and explore the career path for Database Administrator