Back to Plant Bioinformatics
Learner Reviews & Feedback for Plant Bioinformatics by University of Toronto
227 ratings
About the 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 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
Top reviews
SS
Sep 14, 2022
That was so insightful and learning course about plants bioinformatic out of basic methods.
Also help in working project to give meaningful answers with validation
DD
May 5, 2020
In- depth learning of the various tools and softwares available to study plant bioinformatics. Guidance of the author through the labs is insightful and informative.
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