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4.7
200 個評分
39 個審閱

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初級

完成時間大約為11 小時

建議:12-18 hours of videos and labs...

英語(English)

字幕:英語(English)

100% 在線

立即開始,按照自己的計劃學習。

可靈活調整截止日期

根據您的日程表重置截止日期。

初級

完成時間大約為11 小時

建議:12-18 hours of videos and labs...

英語(English)

字幕:英語(English)

教學大綱 - 您將從這門課程中學到什麼

1
完成時間為 3 小時

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 個視頻 (總計 34 分鐘), 4 個閱讀材料, 1 個測驗
4 個視頻
Lecture21分鐘
Lab Discussion9分鐘
Summary1分鐘
4 個閱讀材料
Acknowledgements10分鐘
Course Logistics10分鐘
Lecture Materials10分鐘
Lab 1 -- Protein Domain, Motif and Profile Analysis30分鐘
1 個練習
Lab 1 Quiz6分鐘
2
完成時間為 2 小時

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 個視頻 (總計 37 分鐘), 2 個閱讀材料, 1 個測驗
4 個視頻
Lecture23分鐘
Lab Discussion11分鐘
Summary1分鐘
2 個閱讀材料
Lecture Materials10分鐘
Lab 2 -- Protein-Protein Interactions30分鐘
1 個練習
Lab 2 Quiz6分鐘
3
完成時間為 2 小時

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 個視頻 (總計 32 分鐘), 2 個閱讀材料, 1 個測驗
4 個視頻
Lecture13分鐘
Lab Discussion16分鐘
Summary1分鐘
2 個閱讀材料
Lecture Materials10分鐘
Lab 3 -- Structural Bioinformatics30分鐘
1 個練習
Lab 3 Quiz6分鐘
4
完成時間為 10 分鐘

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

...
1 個測驗
1 個練習
Quiz: Protein Motifs, Protein-Protein Interactions, and Protein Structure10分鐘
5
完成時間為 3 小時

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 個視頻 (總計 49 分鐘), 2 個閱讀材料, 1 個測驗
4 個視頻
Lecture26分鐘
Lab Discusssion19分鐘
Summary1分鐘
2 個閱讀材料
Lecture Materials10分鐘
Lab 4 -- Gene Expression Analysis I30分鐘
1 個練習
Lab 4 Quiz6分鐘
6
完成時間為 2 小時

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 個視頻 (總計 42 分鐘), 2 個閱讀材料, 1 個測驗
5 個視頻
Lecture part 120分鐘
Lecture part 27分鐘
Lab Discussion12分鐘
Summary34
2 個閱讀材料
Lecture Materials10分鐘
Lab 5 -- Gene Expression Data Analysis II30分鐘
1 個練習
Lab 5 Quiz6分鐘
7
完成時間為 2 小時

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 個視頻 (總計 40 分鐘), 2 個閱讀材料, 1 個測驗
4 個視頻
Lecture22分鐘
Lab Discussion15分鐘
Summary57
2 個閱讀材料
Lecture Materials10分鐘
Lab 6 -- Cis Regulatory Element Mapping and Prediction30分鐘
1 個練習
Lab 6 Quiz6分鐘
8
完成時間為 1 小時

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

...
1 個閱讀材料, 2 個測驗
1 個閱讀材料
Final Assignment Instructions10分鐘
2 個練習
Quiz: Modules 5-710分鐘
Final Assignment10分鐘
4.7
39 個審閱Chevron Right

20%

完成這些課程後已開始新的職業生涯

25%

通過此課程獲得實實在在的工作福利

11%

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創建者 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

創建者 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.

講師

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Nicholas James Provart

Professor
Cell & Systems Biology

關於 多伦多大学

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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