课程概述
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 2025]:
Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA, SUBA5 and Cell eFP Browser, 1001 Genomes Browser, PlantConnectome
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, SCEA and Ecker Lab Seed-to-Seed scAtlas
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
热门审阅
QR
Mar 9, 2019
Very good course for mastering bioinformatics skills. Genetics and molecular biology students/professionals should take this course to augment their research skills.
SK
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.
筛选依据：
51 - Plant Bioinformatics 的 51 个评论（共 51 个）
创建者 waleed h
•May 28, 2023
this course is beneficial for me