Plant Bioinformatics

About this Course

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 2024]: Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA; SUBA5 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

Created by: University of Toronto


Related Online Courses

In this course, you will see how to use advanced machine-learning techniques to build more sophisticated recommender systems. Machine Learning is able to provide recommendations and make better... more
If you want to learn how to make a living with your music, this is the course for you. How to Make Money with Your Music Copyrights will provide an overview of basic copyright principles and their... more
This is a self-paced lab that takes place in the Google Cloud console. This lab shows how to use Cloud Data Fusion to explore data lineage - the data\'s origins and its movement over time.Created... more
About the course\\n\\nThis specialization is for anyone who would like to improve how their company or organization impacts the environment, people and communities. We will introduce you to some of... more
This is a Google Cloud Self-Paced Lab. In this lab, you\'ll learn the best methods to optimize query performance in Looker. Looker is a modern data platform in Google Cloud that you can use to... more

CONTINUE SEARCH

FOLLOW COLLEGE PARENT CENTRAL