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Plant Bioinformatics
  • Level Professional
  • Duration 14 hours
  • Course by University of Toronto
  • Offered by

About

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. For instance, knowing where and when a gene is expressed can help us narrow down the phenotypic search space when we don't see a phenotype in a gene mutant under "normal" growth conditions. Coexpression analyses and association networks can provide high-quality candidate genes involved in a biological process of interest. Using Gene Ontology enrichment analysis and pathway visualization tools can help us make sense of our own 'omics experiments and answer the question "what processes/pathways are being perturbed in our mutant of interest?" Structure: each of the 6 week hands-on modules consists of a ~2 minute intro, a ~20 minute theory mini-lecture, a 1.5 hour hands-on lab, an optional ~20 minute lab discussion if experiencing difficulties with lab, and a ~2 minute summary. Tools covered [Material updated in June 2023]: Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA; SUBA4 and Cell eFP Browser, 1001 Genomes Browser Module 2: EXPRESSION TOOLS. eFP Browser / eFP-Seq Browser, Araport, ARDB, TravaDB, NCBI Genome Data Viewer for exploring RNA-seq data for many plant species, MPSS database for small RNAs Module 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2 Module 4: PROMOTER ANALYSIS. Cistome, MEME, ePlant Module 5: GO ENRICHMENT ANALYSIS AND PATHWAY VIZUALIZATION. AgriGO, AmiGO, Classification SuperViewer, TAIR, g:profiler, AraCyc, MapMan (optional: Plant Reactome) Module 6: NETWORK EXPLORATION. Arabidopsis Interactions Viewer 2, ePlant, TF2Network, Virtual Plant, GeneMANIA

Modules

Plant Genomic Databases and Useful Sites for Information about Proteins

    • 2 Videos
    • 3 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

3 Readings

  • Acknowledgements
  • Course Logistics
  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 1

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 1 -- Plant Genomic Databases and Tools for Exploring Protein Information

Expression Analysis

    • 2 Videos
    • 1 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

1 Readings

  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 2

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 2 -- Expression Analysis

Coexpression Tools

    • 2 Videos
    • 1 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

1 Readings

  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 3

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 3 -- Coexpression Tools

Sectional Quiz 1

    • 1 Assignment
Show info about module content

1 Assignment

  • Sectional Quiz 1

Promoter Analysis

    • 2 Videos
    • 1 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

1 Readings

  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 4

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 4 -- Promoter Analysis

Functional Classification and Pathway Visualization

    • 2 Videos
    • 1 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

1 Readings

  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 5

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 5 -- Functional Classification and Pathway Visualization

Network Exploration (PPIs, PDIs, GRNs)

    • 2 Videos
    • 1 Readings
Show info about module content

2 Videos

  • Introduction
  • Mini-lecture

1 Readings

  • Mini-lecture Notes

Lab and Summary

    • 2 Videos
    • 1 Readings
    • 1 Assignment
Show info about module content

1 Assignment

  • Lab Quiz 6

2 Videos

  • Lab Discussion
  • Summary

1 Readings

  • Lab 6 -- Network Exploration (PPIs, PDIs, GRNs)

Sectional Quiz 2

    • 1 Assignment
Show info about module content

1 Assignment

  • Sectional Quiz 2

Final Assignment

    • 1 Assignment
Show info about module content

1 Assignment

  • Final Assignment

Auto Summary

**Course Overview: Plant Bioinformatics** Immerse yourself in the transformative world of plant biology with the "Plant Bioinformatics" course, designed for professionals in the Health & Fitness domain. Over the past decade and a half, significant advancements in plant genomics and bioinformatics have revolutionized the field, making it possible to sequence plant genomes, profile transcriptomes, and analyze protein interactions with unprecedented ease and accuracy. **Instructor:** This course is offered by Coursera and is tailored to provide an in-depth understanding of various bioinformatics tools and techniques essential for modern plant biology research. **Course Structure and Content:** The course spans six weeks, featuring hands-on modules that blend theory and practical lab sessions: - **Module 1:** Dive into genomic databases and protein tools, exploring resources like Araport, TAIR, and PLAZA. - **Module 2:** Learn about expression tools and RNA-seq data exploration through platforms such as eFP Browser and NCBI Genome Data Viewer. - **Module 3:** Gain insights into coexpression tools including ATTED II and AraNet. - **Module 4:** Focus on promoter analysis using tools like Cistome and MEME. - **Module 5:** Master gene ontology enrichment analysis and pathway visualization with AgriGO and MapMan. - **Module 6:** Explore network visualization and interaction tools like Arabidopsis Interactions Viewer 2 and GeneMANIA. Each module includes a concise introduction, a detailed mini-lecture, an extensive hands-on lab, an optional discussion session for additional support, and a brief summary to consolidate learning. **Duration and Subscription:** The entire course is designed to be completed in approximately 14 hours, making it a comprehensive yet manageable commitment for busy professionals. It is available with a Starter subscription, ensuring accessible entry into advanced plant bioinformatics studies. **Target Audience:** This course is ideal for professionals and researchers in plant biology, genetics, and related fields who seek to enhance their bioinformatics skills and apply cutting-edge tools to their research. Whether you're looking to understand gene expression patterns, perform coexpression analyses, or visualize complex biological pathways, this course provides the expertise needed to excel in the rapidly evolving domain of plant bioinformatics. Join us on this educational journey and unlock the potential of bioinformatics in advancing your plant biology research.

Nicholas James Provart
Instructor

Nicholas James Provart