このコースについて
4,735

100%オンライン

自分のスケジュールですぐに学習を始めてください。

柔軟性のある期限

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中級レベル

None required but you should be familiar with basic aspects of plant and molecular biology. Bioinformatic Methods I and II would be good preparation

約11時間で修了

推奨:6 weeks of hands-on study, plus 2 evaluation weeks. The hands-on modules will take 2-4 hours of time...

英語

字幕:英語

100%オンライン

自分のスケジュールですぐに学習を始めてください。

柔軟性のある期限

スケジュールに従って期限をリセットします。

中級レベル

None required but you should be familiar with basic aspects of plant and molecular biology. Bioinformatic Methods I and II would be good preparation

約11時間で修了

推奨:6 weeks of hands-on study, plus 2 evaluation weeks. The hands-on modules will take 2-4 hours of time...

英語

字幕:英語

シラバス - 本コースの学習内容

1
3時間で修了

Plant Genomic Databases, and useful sites for info about proteins

In this module we'll be exploring several plant databases including Ensembl Plants, Gramene, PLAZA, SUBA, TAIR and Araport. The information in these databases allows us to easily identify functional regions within gene products, view subcellular localization, find homologs in other species, and even explore pre-computed gene trees to see if our gene of interest has undergone a gene duplication event in another species, all at the click of a mouse!...
4件のビデオ (合計44分), 4 readings, 1 quiz
4件のビデオ
Mini-lecture17 分
Lab Discussion23 分
Summary1 分
4件の学習用教材
Acknowledgements10 分
Course Logistics10 分
Mini-lecture Notes10 分
Lab 1 -- Plant Genomic Databases and Tools for Exploring Protein Information30 分
1の練習問題
Lab Quiz 1
2
2時間で修了

Expression Analysis

Vast databases of gene expression and nifty visualization tools allow us to explore where and when a gene is expressed. Often this information can be used to help guide a search for a phenotype if we don't see a phenotype in a gene mutant under "normal" growth conditions. We explore several tools for Arabidopsis data (eFP Browser, Genevestigator, TraVA DB, Araport) along with NCBI's Genome Data Viewer for RNA-seq data for other plant species. We also examine the MPSS database of small RNAs and degradation products to see if our example gene has any potential microRNA targets....
4件のビデオ (合計38分), 2 readings, 1 quiz
4件のビデオ
Mini-lecture17 分
Lab Discussion18 分
Summary50
2件の学習用教材
Mini-lecture Notes10 分
Lab 2 -- Expression Analysis30 分
1の練習問題
Lab Quiz 2
3
2時間で修了

Coexpression Tools

Being able to group genes by similar patterns of expression across expression data sets using algorithms like WGCNA is a very useful way of organizing the data. Clusters of genes with similar patterns of expression can then be subject to Gene Ontology term enrichment analysis (see Module 5) or examined to see if they are part of the same pathway. What's even more powerful is being able to identify genes with similar patterns of expression without doing a single expression profiling experiment, by mining gene expression databases! There are several tools that allow you to do this in many plant species simply by entering a query gene identifier. The genes that are returned are often in the same biological process as the query gene, and thus this "guilt-by-association" paradigm is a excellent tool for hypothesis generation....
4件のビデオ (合計29分), 2 readings, 1 quiz
4件のビデオ
Mini-lecture9 分
Lab Discussion16 分
Summary49
2件の学習用教材
Mini-lecture Notes10 分
Lab 3 -- Coexpression Tools30 分
1の練習問題
Lab Quiz 3
4

Sectional Quiz 1

...
1 quiz
1の練習問題
Sectional Quiz 1
5
2時間で修了

Promoter Analysis

The regulation of gene expression is one of the main ways by which a plant can control the abundance of a gene product (post-translational modifications and protein degradation are some others). When and where a gene is expressed is controlled to a large extent by the presence of short sequence motifs, called cis-elements, present in the promoter of the gene. These in turn are regulated by transcription factors that perhaps get induced in response to environmental stresses or during specific developmental programs. Thus understanding which transcription factors can bind to which promoters can help us understand the role the downstream genes might be playing in a biological system....
4件のビデオ (合計32分), 2 readings, 1 quiz
4件のビデオ
Mini-lecture17 分
Lab Discussion12 分
Summary49
2件の学習用教材
Mini-lecture Notes10 分
Lab 4 -- Promoter Analysis30 分
1の練習問題
Lab Quiz 4
6
2時間で修了

Functional Classification and Pathway Vizualization

Often the results of 'omics experiments are large lists of genes, such as those that are differentially expressed. We can use a "cherry picking" approach to explore individual genes in those lists but it's nice to be able to have an automated way of analyzing them. Here tools for performing Gene Ontology enrichment analysis are invaluable and can tell you if any particular biological processes or molecular functions are over-represented in your gene list. We'll explore AgriGO, AmiGO, tools at TAIR and the BAR, and g:Profiler, which all allow you to do such analyses. Another useful analysis is to be able to map your gene lists (along with associated e.g. expression values) onto pathway representations, and we'll use AraCyc and MapMan to do this. In this way it is easy to see if certain biosynthetic reactions are upregulated, which can help you interpret your 'omics data!...
4件のビデオ (合計32分), 2 readings, 1 quiz
4件のビデオ
Mini-lecture13 分
Lab Discussion15 分
Summary46
2件の学習用教材
Mini-lecture Notes10 分
Lab 5 -- Functional Classification and Pathway Visualization30 分
1の練習問題
Lab Quiz 5
7
2時間で修了

Network Exploration (PPIs, PDIs, GRNs)

Molecules inside the cell rarely operate in isolation. Proteins act together to form complexes, or are part of signal transduction cascades. Transcription factors bind to cis-elements in promoters or elsewhere and can act as activators or repressors of transcription. MicroRNAs can affect transcription in other ways. One of the main themes to have emerged in the past two decades in biology is that of networks. In terms of protein-protein interaction networks, often proteins that are highly connected with others are crucial for biological function – when these “hubs” are perturbed, we see large phenotypic effects. The way that transcription factors interact with downstream promoters, some driving the expression of other transcription factors that in turn regulate genes combinatorially with upstream transcription factors can have an important biological effect in terms of modulating the kind of output achieved. The tools described in this lab can help us to explore molecular interactions in a network context, perhaps with the eventual goal of modeling the behaviour of a given system....
4件のビデオ (合計34分), 2 readings, 1 quiz
4件のビデオ
Mini-lecture18 分
Lab Discussion13 分
Summary1 分
2件の学習用教材
Mini-lecture Notes10 分
Lab 6 -- Network Exploration (PPIs, PDIs, GRNs)30 分
1の練習問題
Lab Quiz 6
8

Sectional Quiz 2 and Final Assignment

...
2 quizzes
2の練習問題
Sectional Quiz 2
Final Assignment
4.8
8件のレビューChevron Right

人気のレビュー

by QRMar 10th 2019

Very good course for mastering bioinformatics skills. Genetics and molecular biology students/professionals should take this course to augment their research skills.

by FSFeb 22nd 2019

Professor Provart is very good and the labs taught us in simple and direct instructions how to perform a wide range of analysis regarding Plant Bioinformatics.

講師

Avatar

Nicholas James Provart

Professor
Cell & Systems Biology

トロント大学(University of Toronto)について

Established in 1827, the University of Toronto is one of the world’s leading universities, renowned for its excellence in teaching, research, innovation and entrepreneurship, as well as its impact on economic prosperity and social well-being around the globe. ...

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