About this Course
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Beginner Level

Approx. 11 hours to complete

Suggested: 12-18 hours of videos and labs...

English

Subtitles: English

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Beginner Level

Approx. 11 hours to complete

Suggested: 12-18 hours of videos and labs...

English

Subtitles: English

Syllabus - What you will learn from this course

Week
1
3 hours to complete

Protein Motifs

In this module we'll be exploring conserved regions within protein families. Such regions can help us understand the biology of a sequence, in that they are likely important for biological function, and also be used to help ascribe function to sequences where we can't identify any homologs in the databases. There are various ways of describing the conserved regions from simple regular expressions to profiles to profile hidden Markov models (HMMs).

...
4 videos (Total 34 min), 4 readings, 1 quiz
4 videos
Lecture21m
Lab Discussion9m
Summary1m
4 readings
Acknowledgements10m
Course Logistics10m
Lecture Materials10m
Lab 1 -- Protein Domain, Motif and Profile Analysis1h 30m
1 practice exercise
Lab 1 Quiz6m
Week
2
2 hours to complete

Protein-Protein Interactions

In this module we'll be exploring protein-protein interactions (PPIs). Protein-protein interactions are important as proteins don't act in isolation, and often an examination of the interaction partners (determined in an unbiased, perhaps high throughput way) of a given protein can tell us a lot about its biology. We'll talk about some different methods used to determine PPIs and go over their strengths and weaknesses. In the lab we'll use 3 different tools and two different databases to examine interaction partners of BRCA2, a protein that we examined in last module's lab. Finally, we'll touch on a "foundational" concept, Gene Ontology (GO) term enrichment analysis, to help us understand in an overview way the proteins interacting with our example.

...
4 videos (Total 37 min), 2 readings, 1 quiz
4 videos
Lecture23m
Lab Discussion11m
Summary1m
2 readings
Lecture Materials10m
Lab 2 -- Protein-Protein Interactions1h 30m
1 practice exercise
Lab 2 Quiz6m
Week
3
2 hours to complete

Protein Structure

The determination of a protein's tertiary structure in three dimensions can tell us a lot about the biology of that protein. In this module's mini-lecture, we'll talk about some different methods used to determine a protein's tertiary structure and cover the main database for protein structure data, the PDB. In the lab we'll explore the PDB and an online tool for searching for structural (as opposed to sequence) similarity, VAST. We'll then use a nice piece of stand-alone software, PyMOL, to explore several protein structures in more detail.

...
4 videos (Total 32 min), 2 readings, 1 quiz
4 videos
Lecture13m
Lab Discussion16m
Summary1m
2 readings
Lecture Materials10m
Lab 3 -- Structural Bioinformatics1h 30m
1 practice exercise
Lab 3 Quiz6m
Week
4
10 minutes to complete

Review: Protein Motifs, Protein-Protein Interactions, and Protein Structure

...
1 quiz
1 practice exercise
Quiz: Protein Motifs, Protein-Protein Interactions, and Protein Structure10m
Week
5
3 hours to complete

Gene Expression Analysis I

When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Several different methods exist for generating gene expression levels for all of the genes in the genome in tissues or even at cell-type-specific resolution. In this class we'll be processing and then examining some gene expression data generated using RNA-seq. We'll explore one of the main databases for RNA-seq expression data, the Sequence Read Archive (SRA), and then use an open-source suite of programs in R called BioConductor to process the raw reads from 4 RNA-seq data sets, to summarize their expression levels, to select significantly differentially expressed genes, and finally to visualize these as a heat map.

...
4 videos (Total 49 min), 2 readings, 1 quiz
4 videos
Lecture26m
Lab Discusssion19m
Summary1m
2 readings
Lecture Materials10m
Lab 4 -- Gene Expression Analysis I1h 30m
1 practice exercise
Lab 4 Quiz6m
Week
6
2 hours to complete

Gene Expression Analysis II

When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Several different methods exist for generating gene expression levels for all of the genes in the genome in tissues or even at cell-type-specific resolution. In this class we'll be hierarchically clustering our significantly differentially expressed genes from last time using BioConductor and the built-in function of an online tool, called Expression Browser. Then we'll be using another online tool that uses a similarity metric, the Pearson correlation coefficient, to identify genes responding in a similar manner to our gene of interest, in this case AP3. We'll use a second tool, ATTED-II to corroborate our gene list. We'll also be exploring some online databases of gene expression and an online tool for doing a Gene Ontology enrichment analysis.

...
5 videos (Total 42 min), 2 readings, 1 quiz
5 videos
Lecture part 120m
Lecture part 27m
Lab Discussion12m
Summary34s
2 readings
Lecture Materials10m
Lab 5 -- Gene Expression Data Analysis II1h 30m
1 practice exercise
Lab 5 Quiz6m
Week
7
2 hours to complete

Cis Regulatory Systems

When and where genes are expressed in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Gene expression is controlled in part by the presence of short sequences in the promoters (and other parts) of genes, called cis-elements, which permit transcription factors and other regulatory proteins to bind to direct the patterns of expression in certain tissues or cells or in response to environmental stimuli: We'll explore a couple of sets of promoters of genes that are coexpressed with AP3 from Arabidopsis, and with INSULIN from human, for the presence of known cis-elements, and we'll also try to predict some new ones using a couple of different methods.

...
4 videos (Total 40 min), 2 readings, 1 quiz
4 videos
Lecture22m
Lab Discussion15m
Summary57s
2 readings
Lecture Materials10m
Lab 6 -- Cis Regulatory Element Mapping and Prediction1h 30m
1 practice exercise
Lab 6 Quiz6m
Week
8
1 hour to complete

Review: Gene Expression Analysis and Cis Regulatory Systems + Final Assignment

...
1 reading, 2 quizzes
1 reading
Final Assignment Instructions10m
2 practice exercises
Quiz: Modules 5-710m
Final Assignment10m
4.7
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Top reviews from Bioinformatic Methods II

By RGApr 6th 2017

Gives the student real world exposure to the tools to study proteins gene regulation, etc. Instructor is involved and friendly. Highly recommended for someone who is interested in contemporary

By NMJan 9th 2018

Hi Nicholas, Thank you so much for giving a lot of information. Bioinformatic Methods II was little difficult but understood after repeating the lad discussions. Thanks a lot.

Instructor

Avatar

Nicholas James Provart

Professor
Cell & Systems Biology

About 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. ...

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