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所在平台: Coursera |
课程主页: https://www.coursera.org/learn/plant-bioinformatics-capstone
课程评论：没有评论
课程名称：植物生物信息学顶点项目 概述：过去15年，植物生物学取得了令人兴奋的进展。数百种植物基因组已被测序，RNA-seq技术使得全转录组表达谱分析成为可能，而大量基于“-seq”的方法则以便宜的高通量方式确定了蛋白质-蛋白质和蛋白质-DNA的相互作用。这些数据集使我们能够轻松生成假设。 在Coursera上的植物生物信息学课程中，我们介绍了33种植物特定的在线工具，从基因组浏览器到转录组数据挖掘、启动子/网络分析等。在植物生物信息学顶点项目中，我们将利用这些工具假设一个未知功能基因的生物学角色，并总结成书面实验报告。 该课程是Coursera的植物生物信息学专业的一部分，介绍了核心的生物信息学能力和资源，例如NCBI的Genbank、Blast、多序列比对、系统发育等。此外，植物生物信息学的特定概念和工具也在该课程中得到了介绍。 课程大纲： 1. **探索您的感兴趣基因**：使用阿拉伯芥中的一个（大部分）未知功能的基因At3g20300，利用在线数据库收集有关该基因的信息，分析其大小、同源基因、系统发育关系、功能域信息和亚细胞定位，以及基因表达数据库中该基因的表达位置。 2. **识别与您的感兴趣基因相关的基因**：通过共表达分析，探索与At3g20300共表达的基因，并寻找这些共表达基因的共同顺式调控基序。 3. **分析您的感兴趣基因及其基因网络的功能**：进行基因本体富集分析，推断未知功能基因的角色，并使用其他网络工具调查与其他基因的额外联系。 4. **实验报告草稿**：将上述分析的信息综合成实验报告草稿，描述我们感兴趣基因的潜在功能，结合文献对相关基因的介绍，并提出实验以验证我们的假设。 5. **实验报告最终稿**：根据同伴评审的反馈，完善草稿，提交最终报告，报告长度应为13-15页（双倍行距），包括插图。 本课程得到了多伦多大学艺术与科学学院开放课程倡议基金（OCIF）的资助，由Eddi Esteban、Will Heikoop和Nicholas Provart实施，并由Asher Pasha编程开发了基因ID随机生成器。
Name:Exploring your gene of interest with online databases
Description:In the Week 1 module, we are going to use an example gene of (mostly) unknown function from Arabidopsis, At3g20300, and see what online databases can tell us about that gene. Part A uses tools that we have explored in Plant Bioinformatics to gather information about the gene/gene product, such as its size, what its homologs are, phylogenetic relationship to other sequences, domain information, and subcellular localization. Part B explores gene expression databases to see where that gene is expressed. Often where and when a gene is expressed can give us clues as to its function.
Name:Identifying genes related to your gene of interest
Description:Often the function of genes that are coexpressed with a gene of unknown function can give us hints about the function of that gene. Researchers are now often using coexpression analyses as “primary screens” to identify “new” genes in biological pathways (a few examples are described in Usadel et al., 2009). Another interesting facet is whether the promoters of these sets of coexpressed genes contain any common cis-regulatory motifs. In Part A, we’ll explore the genes that are coexpressed with At3g20300, and in Part B, we’ll look for common regulatory motifs.
Name:Analysis of the function of your gene of interest and its network of genes
Description:Gene Ontology enrichment analysis for a set of coexpressed gene is often useful for figuring out what that group of genes is doing. By doing such analyses with a set of coexpressed genes can we infer a role for our gene of unknown function? We'll explore this aspect in Part A, along with investigating potential pathways the gene list is involved in. In Part B, we'll use other network tools to investigate additional linkages to other genes, above and beyond those suggested by coexpression. It is sometimes useful to investigate these too! Again, we'll be using At3g20300 as our example.
Name:Lab report draft
Description:Now we will take the above analyses and synthesize the information from them into a draft lab report/essay describing the putative function of our gene of interest with unknown function. We'll draw on the literature to describe what is known about related genes, and propose some experiments to test our hypotheses about our gene's potential function.
Name:Final copy of lab report
Description:Based on feedback from peer reviews, we'll polish our draft to submit a final report! The report should be around 13-15 pages long (double spaced) including figures, which should be included inline. The page count does not include Methods or References (see Example Essay for format).
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 or tap of a finger. In Plant Bioinformatics on Coursera.org, we covered 33 plant-specific online tools from genome browsers to transcriptomic data mining to promoter/network analyses and others, and in this Plant Bioinformatics Capstone we'll use these tools to hypothesize a biological role for a gene of unknown function, summarized in a written lab report. This course is part of a Plant Bioinformatics Specialization on Coursera, which introduces core bioinformatic competencies and resources, such as NCBI's Genbank, Blast, multiple sequence alignments, phylogenetics in Bioinformatic Methods I, followed by protein-protein interactions, structural bioinformatics and RNA-seq analysis in Bioinformatic Methods II, in addition to the plant-specific concepts and tools introduced in Plant Bioinformatics and the Plant Bioinformatics Capstone. This course/capstone was developed with funding from the University of Toronto's Faculty of Arts and Science Open Course Initiative Fund (OCIF) and was implemented by Eddi Esteban, Will Heikoop and Nicholas Provart. Asher Pasha programmed a gene ID randomizer.
