About this Course
4.9
16 ratings
5 reviews

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Start instantly and learn at your own schedule.

Flexible deadlines

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Intermediate Level

None required but you should be familiar with basic aspects of plant and molecular biology. Bioinformatic Methods I and II would be good preparation

Approx. 12 hours to complete

Suggested: 6 weeks of hands-on study, plus 2 evaluation weeks. The hands-on modules will take 2-4 hours of time...

English

Subtitles: English

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Intermediate Level

None required but you should be familiar with basic aspects of plant and molecular biology. Bioinformatic Methods I and II would be good preparation

Approx. 12 hours to complete

Suggested: 6 weeks of hands-on study, plus 2 evaluation weeks. The hands-on modules will take 2-4 hours of time...

English

Subtitles: English

Syllabus - What you will learn from this course

Week
1
3 hours to complete

Plant Genomic Databases, and useful sites for info about proteins

In this module we'll be exploring several plant databases including Ensembl Plants, Gramene, PLAZA, SUBA, TAIR and Araport. The information in these databases allows us to easily identify functional regions within gene products, view subcellular localization, find homologs in other species, and even explore pre-computed gene trees to see if our gene of interest has undergone a gene duplication event in another species, all at the click of a mouse!...
4 videos (Total 44 min), 4 readings, 1 quiz
4 videos
Mini-lecture17m
Lab Discussion23m
Summary1m
4 readings
Acknowledgements10m
Course Logistics10m
Mini-lecture Notes10m
Lab 1 -- Plant Genomic Databases and Tools for Exploring Protein Information30m
1 practice exercise
Lab Quiz 1
Week
2
2 hours to complete

Expression Analysis

Vast databases of gene expression and nifty visualization tools allow us to explore where and when a gene is expressed. Often this information can be used to help guide a search for a phenotype if we don't see a phenotype in a gene mutant under "normal" growth conditions. We explore several tools for Arabidopsis data (eFP Browser, Genevestigator, TraVA DB, Araport) along with NCBI's Genome Data Viewer for RNA-seq data for other plant species. We also examine the MPSS database of small RNAs and degradation products to see if our example gene has any potential microRNA targets....
4 videos (Total 38 min), 2 readings, 1 quiz
4 videos
Mini-lecture17m
Lab Discussion18m
Summary50s
2 readings
Mini-lecture Notes10m
Lab 2 -- Expression Analysis30m
1 practice exercise
Lab Quiz 2
Week
3
2 hours to complete

Coexpression Tools

Being able to group genes by similar patterns of expression across expression data sets using algorithms like WGCNA is a very useful way of organizing the data. Clusters of genes with similar patterns of expression can then be subject to Gene Ontology term enrichment analysis (see Module 5) or examined to see if they are part of the same pathway. What's even more powerful is being able to identify genes with similar patterns of expression without doing a single expression profiling experiment, by mining gene expression databases! There are several tools that allow you to do this in many plant species simply by entering a query gene identifier. The genes that are returned are often in the same biological process as the query gene, and thus this "guilt-by-association" paradigm is a excellent tool for hypothesis generation....
4 videos (Total 29 min), 2 readings, 1 quiz
4 videos
Mini-lecture9m
Lab Discussion16m
Summary49s
2 readings
Mini-lecture Notes10m
Lab 3 -- Coexpression Tools30m
1 practice exercise
Lab Quiz 3
Week
4

Sectional Quiz 1

...
1 quiz
1 practice exercise
Sectional Quiz 1
4.9
5 ReviewsChevron Right

Top Reviews

By QRMar 10th 2019

Very good course for mastering bioinformatics skills. Genetics and molecular biology students/professionals should take this course to augment their research skills.

By FSFeb 22nd 2019

Professor Provart is very good and the labs taught us in simple and direct instructions how to perform a wide range of analysis regarding Plant Bioinformatics.

Instructor

Avatar

Nicholas James Provart

Professor
Cell & Systems Biology

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