Module: Plant Bioinformatics
CSB1021H/S, Teaching Section LEC 0139
Coordinator: Professor Nicholas Provart
Offered: Fall 2024, from mid-October to late November
Weight: One module (0.25 FCE)
Time: TBA
Location: Earth Sciences Centre. St. George campus (room TBA)
Enrollment: Limit of 8 students
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 classes will draw on material from Prof. Provart’s two Plant Bioinformatics courses running on Coursera.org – Plant Bioinformatics and the Plant Bioinformatics Capstone. Tools explored will include those listed below. We expect to cover around 2 “modules” (in the Courserian sense) per class, with the classes towards the end taken up with capstone presentations.
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, Genevestigator, TravaDB, NCBI Genome Data Viewer for exploring RNA-seq data for many plant species other than Arabidopsis, MPSS database for small RNAs
Module 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2
Module 4: PROMOTER ANALYSIS. Cistome, Athena, 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
Grading will be based on participation (20%), a tools presentation (20%), a written report (capstone paper; 35%), and a final presentation (25%)
Last updated on August 9th, 2024