Über diesen Kurs
4,715

100 % online

Beginnen Sie sofort und lernen Sie in Ihrem eigenen Tempo.

Flexible Fristen

Setzen Sie Fristen gemäß Ihrem Zeitplan zurück.

Stufe „Mittel“

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

Ca. 11 Stunden zum Abschließen

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

Englisch

Untertitel: Englisch

100 % online

Beginnen Sie sofort und lernen Sie in Ihrem eigenen Tempo.

Flexible Fristen

Setzen Sie Fristen gemäß Ihrem Zeitplan zurück.

Stufe „Mittel“

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

Ca. 11 Stunden zum Abschließen

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

Englisch

Untertitel: Englisch

Lehrplan - Was Sie in diesem Kurs lernen werden

Woche
1
3 Stunden zum Abschließen

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 Videos (Gesamt 44 min), 4 Lektüren, 1 Quiz
4 Videos
Mini-lecture17m
Lab Discussion23m
Summary1m
4 Lektüren
Acknowledgements10m
Course Logistics10m
Mini-lecture Notes10m
Lab 1 -- Plant Genomic Databases and Tools for Exploring Protein Information30m
1 praktische Übung
Lab Quiz 1
Woche
2
2 Stunden zum Abschließen

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 Videos (Gesamt 38 min), 2 Lektüren, 1 Quiz
4 Videos
Mini-lecture17m
Lab Discussion18m
Summary50
2 Lektüren
Mini-lecture Notes10m
Lab 2 -- Expression Analysis30m
1 praktische Übung
Lab Quiz 2
Woche
3
2 Stunden zum Abschließen

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 Videos (Gesamt 29 min), 2 Lektüren, 1 Quiz
4 Videos
Mini-lecture9m
Lab Discussion16m
Summary49
2 Lektüren
Mini-lecture Notes10m
Lab 3 -- Coexpression Tools30m
1 praktische Übung
Lab Quiz 3
Woche
4

Sectional Quiz 1

...
1 Quiz
1 praktische Übung
Sectional Quiz 1
Woche
5
2 Stunden zum Abschließen

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 Videos (Gesamt 32 min), 2 Lektüren, 1 Quiz
4 Videos
Mini-lecture17m
Lab Discussion12m
Summary49
2 Lektüren
Mini-lecture Notes10m
Lab 4 -- Promoter Analysis30m
1 praktische Übung
Lab Quiz 4
Woche
6
2 Stunden zum Abschließen

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 Videos (Gesamt 32 min), 2 Lektüren, 1 Quiz
4 Videos
Mini-lecture13m
Lab Discussion15m
Summary46
2 Lektüren
Mini-lecture Notes10m
Lab 5 -- Functional Classification and Pathway Visualization30m
1 praktische Übung
Lab Quiz 5
Woche
7
2 Stunden zum Abschließen

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 Videos (Gesamt 34 min), 2 Lektüren, 1 Quiz
4 Videos
Mini-lecture18m
Lab Discussion13m
Summary1m
2 Lektüren
Mini-lecture Notes10m
Lab 6 -- Network Exploration (PPIs, PDIs, GRNs)30m
1 praktische Übung
Lab Quiz 6
Woche
8

Sectional Quiz 2 and Final Assignment

...
2 Quiz
2 praktische Übungen
Sectional Quiz 2
Final Assignment
4.8
8 BewertungenChevron Right

Top-Bewertungen

von 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.

von 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.

Dozent

Avatar

Nicholas James Provart

Professor
Cell & Systems Biology

Über University of Toronto

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. ...

Häufig gestellte Fragen

  • Sobald Sie sich für ein Zertifikat angemeldet haben, haben Sie Zugriff auf alle Videos, Quizspiele und Programmieraufgaben (falls zutreffend). Aufgaben, die von anderen Kursteilnehmern bewertet werden, können erst dann eingereicht und überprüft werden, wenn Ihr Unterricht begonnen hat. Wenn Sie sich den Kurs anschauen möchten, ohne ihn zu kaufen, können Sie womöglich auf bestimmte Aufgaben nicht zugreifen.

  • Wenn Sie ein Zertifikat erwerben, erhalten Sie Zugriff auf alle Kursmaterialien, einschließlich bewerteter Aufgaben. Nach Abschluss des Kurses wird Ihr elektronisches Zertifikat zu Ihrer Seite „Errungenschaften“ hinzugefügt – von dort können Sie Ihr Zertifikat ausdrucken oder es zu Ihrem LinkedIn Profil hinzufügen. Wenn Sie nur lesen und den Inhalt des Kurses anzeigen möchten, können Sie kostenlos als Gast an dem Kurs teilnehmen.

Haben Sie weitere Fragen? Besuchen Sie das Hilfe-Center für Teiln..