{"id":8807,"date":"2022-04-28T21:17:36","date_gmt":"2022-04-28T21:17:36","guid":{"rendered":"https:\/\/www.tun.com\/courses\/2019\/12\/23\/plant-bioinformatics\/"},"modified":"2022-04-28T21:17:36","modified_gmt":"2022-04-28T21:17:36","slug":"plant-bioinformatics","status":"publish","type":"post","link":"https:\/\/www.tun.com\/courses\/plant-bioinformatics\/university-of-toronto\/","title":{"rendered":"Plant Bioinformatics"},"content":{"rendered":"
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Description<\/h2>\n

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?”<\/p>\n

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.<\/p>\n

Tools covered:
\nModule 1: GENOMIC DBs \/ PRECOMPUTED GENE TREES \/ PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA; SUBA4 and Cell eFP Browser, 1001 Genomes Browser
\nModule 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
\nModule 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2
\nModule 4: PROMOTER ANALYSIS. Cistome, Athena, ePlant
\nModule 5: GO ENRICHMENT ANALYSIS AND PATHWAY VIZUALIZATION. AgriGO, AmiGO, Classification SuperViewer, TAIR, g:profiler, AraCyc, MapMan (optional: Plant Reactome)
\nModule 6: NETWORK EXPLORATION. Arabidopsis Interactions Viewer 2, ePlant, TF2Network, Virtual Plant, GeneMANIA<\/p>\n

[Material updated in June 2019]<\/p>\n

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Price: Enroll For Free!<\/h2>\n
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View Class<\/a><\/div>\n
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Language:<\/strong> <\/em>English<\/p>\n<\/div>\n

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Subtitles<\/strong>: <\/em>English<\/p>\n<\/div>\n<\/div>\n

Plant Bioinformatics – University of Toronto<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Description 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 […]<\/p>\n","protected":false},"author":1,"featured_media":19415,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"footnotes":""},"categories":[269],"tags":[],"class_list":["post-8807","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-university-of-toronto"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png",379,223,false],"thumbnail":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education-150x150.png",150,150,true],"medium":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education-300x177.png",300,177,true],"medium_large":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png",379,223,false],"large":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png",379,223,false],"1536x1536":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png",379,223,false],"2048x2048":["https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png",379,223,false]},"uagb_author_info":{"display_name":"Axiom Pegasus","author_link":"https:\/\/www.tun.com\/courses\/author\/magic\/"},"uagb_comment_info":0,"uagb_excerpt":"Description 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…","featured_media_src_url":"https:\/\/www.tun.com\/courses\/wp-content\/uploads\/2019\/12\/University-of-Torontoonline-education.png","_links":{"self":[{"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/posts\/8807","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/comments?post=8807"}],"version-history":[{"count":0,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/posts\/8807\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/media\/19415"}],"wp:attachment":[{"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/media?parent=8807"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/categories?post=8807"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.tun.com\/courses\/wp-json\/wp\/v2\/tags?post=8807"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}