[Mandarin workshop]: Gene-set Analysis Workshop

[Gene233]

Abstract

Differential expression analysis is a standard and popular statistical framework in biological research. Differentially expressed genes can be identified by comparing different conditions or treatments. Biologists are often interested in the biological implications of these differentially expressed genes, since they could reveal the latent functions and networks in biological system. Many gene functions have been well-annotated in some knowledgebases, such as GO and KEGG. By mapping and identifying the annotated functions of special gene-sets, we can understand broader impacts of functional analysis.

This workshop will focus on performing gene-set enrichment analysis of transcriptomic data and visualizing the results of enrichment analysis. It will begin with loading data from ExperimentHub using the emtdata and msigdb R/Bioconductor packages. It will demonstrate functional analysis of transcriptomic data using the molecular signatures database (through the msigdb R/Bioconductor package) and a gene-set enrichment method, singscore. Finally, we will perform a graph-based approach to visualize, summarize and interpret results of gene-set enrichment analysis, demonstrating how higher order biological themes can be identified in data using the vissE package.

The workshop will be organized into two broad sections:

1. Molecular phenotyping of individual samples
2. Identifying and visualizing higher-order phenotypes

Language used in the workshop

Mandarin

Convenient day for your Long workshop.

4-5pm 1st Nov, 2021 4-5pm 2nd Nov, 2021

Contact Details

chen.j@wehi.edu.au

Comment field

No response

Checklist

• [X] This workshop has a Bioconductor focus or interest to Bioconductor users/developers.
• [X] I checked and confirmed the BioC Asia 2021 Code of Conduct.
• [X] I understood that it would be desirable for the workshop to be based on this template project.

[kozo2]

@Gene233 Thank you for submitting the abstract. The Assignees will start the review. Once accepted by the Assignees, this issue will be closed and your abstract will be posted on https://biocasia2021.bioconductor.org/ .

[kozo2]

I checked @Gene233 's abstract and the package and repository in this abstract. I accept this abstract. After adding your abstract to https://biocasia2021.bioconductor.org/ , I will send a comment addressed to you again. Thank you for your contribution.

[kozo2]

@Gene233 Can I ask you to tell me your name? If it's a problem to ask for it here, I'll ask for it with email.

[Gene233]

@Gene233 Can I ask you to tell me your name? If it's a problem to ask for it here, I'll ask for it with email. Sure! My name is Jinjin Chen. BTW, would you mind telling me when and where shall I upload my workshop? I don't know the exact time of my talk.

[kozo2]

@Gene233 Thank you for your name. It doesn't matter if you haven't uploaded the workshop ""materials (==Rmd)"" until just before. You need to upload it to your GitHub repo with following https://github.com/seandavi/BuildABiocWorkshop . However, the workshop ""Docker image"" is not in time just before, so I would like you to upload it to your Docker Hub around October 18th.

If you often have the opportunity to talk to @XueyiDong , I'll leave it to Xueyi to explain how to do it. But if not, please let me know as I will give you a more detailed explanation (about BuildABiocWorkshop).

[kozo2]

@Gene233 And I will set the date and time of your workshop to 4-5pm 1st Nov, 2021. Please let me know if you have any problems.

[XueyiDong]

It will be 6-7pm Melbourne time. I'm happy to assist with the workshop material.

[kozo2]

I'm sorry, I forgot the time difference and wrote the time in Tokyo. Thank you @XueyiDong Then, I would like ask you to assist with @Gene233 's workshop material. However, if you have any questions, please feel free to contact me.

[Gene233]

Many thanks!

[kozo2]

@Gene233 Can I ask you to give me your name and abstract also in Mandarin?

[kozo2]

@Gene233 The workshop schedule has been decided. Please check it at https://biocasia2021.bioconductor.org/workshops/ .

[Gene233]

@Gene233 Can I ask you to give me your name and abstract also in Mandarin?

Sure! My name is 陈金金. The abstract is as below: 差异表达分析是生物研究中的一项标准且常用的分析手段。通过比较不同条件或者不同处理下的样本，我们可以得到一些列差异表达基因。生物学家们往往对这些基因背后蕴含的生物学意义很感兴趣，因为这些信息可能有助于揭示生物学系统中潜在的功能和网络。很多基因在相关的知识库中得到了良好的注释，比如GO和KEGG。通过将得到的特殊基因集比对到这些已有的数据库来获取相关注释信息，我们可以理解功能分析的更广泛的影响。

本次workshop将着重于演示基于转录组数据的基因集富集分析和对富集分析结果进行可视化。流程的最开始，我们将使用emtdata和msigdb从ExperimentHub中载入数据。本次流程还将演示如何使用分子标志数据库（通过msigdb R包）和基因集富集分析方法（sings core）来对转录组数据进行功能分析。最后，我们将使用一种基于图的方法来可视化、总结并解释基因集富集分析的结果，演示如何使用vissE包在数据中识别更高阶的生物主题。

本次流程将分为两大部分：

1. 单样本的分子表型分型
2. 高阶表型的识别和可视化

[Gene233]

@kozo2 Sorry, there're some tiny mistakes in the previous version of Madarin abstract, here's the revised one: 差异表达分析是生物研究中的一项标准且常用的分析手段。通过比较不同条件或者不同处理下的样本，我们可以得到一系列差异表达基因。生物学家们往往对这些基因背后蕴含的生物学意义很感兴趣，因为这些信息可能有助于揭示生物学系统中潜在的功能和网络。很多基因在相关的知识库中得到了良好的注释，比如GO和KEGG。通过将得到的特殊基因集比对到这些已有的数据库来获取相关注释信息，我们可以理解功能分析的更广泛的影响。

本次workshop将着重于演示基于转录组数据的基因集富集分析和对富集分析结果进行可视化。流程的最开始，我们将使用emtdata和msigdb从ExperimentHub中载入数据。本次流程还将演示如何使用分子标志数据库（通过msigdb R包）和基因集富集分析方法（singscore）来对转录组数据进行功能分析。最后，我们将使用一种基于图的方法来可视化、总结并解释基因集富集分析的结果，演示如何使用vissE包在数据中识别更高阶的生物主题。

本次流程将分为两大部分：

1. 单样本的分子表型分型
2. 高阶表型的识别和可视化

[kozo2]

Thank you @Gene233 I wrote your name and abstract also in Mandarin. https://biocasia2021.bioconductor.org/workshops/ Let me know if you find something that needs update.

[kozo2]

Hi @Gene233 , How is your workshop material going? It needs to be created from https://github.com/seandavi/BuildABiocWorkshop . Please ask me if you need any assistance.

[Gene233]

Hi @Gene233 , How is your workshop material going? It needs to be created from https://github.com/seandavi/BuildABiocWorkshop . Please ask me if you need any assistance.

Hi @kozo2 , We've already uploaded it to the repo and created the docker file. But since there will be some new updates of our relevant packages, we'll update some little changes on Oct 28 and upload a new version to the repo. I think it will be ready before my talk. Or if you're worried about the time, I think we can also upload the current version to Orchestra first and maybe update it when the new version is ready. Our repo is https://davislaboratory.github.io/GenesetAnalysisWorkflow/. We'll update it on Oct 28. Hope it could be helpful.

[Gene233]

Hi @Gene233 , How is your workshop material going? It needs to be created from https://github.com/seandavi/BuildABiocWorkshop . Please ask me if you need any assistance.

Hi @kozo2 , We've already uploaded it to the repo and created the docker file. But since there will be some new updates of our relevant packages, we'll update some little changes on Oct 28 and upload a new version to the repo. I think it will be ready before my talk. Or if you're worried about the time, I think we can also upload the current version to Orchestra first and maybe update it when the new version is ready. Our repo is https://davislaboratory.github.io/GenesetAnalysisWorkflow/. We'll update it on Oct 28. Hope it could be helpful.

Hi @kozo2 , Sorry, the previous link is the demonstration website, the actual repo link is this: https://github.com/DavisLaboratory/GenesetAnalysisWorkflow.git.

[kozo2]

@Gene233 Thank you for the information. I can understand your situation. I don't think it's a problem if there is an update later. So I ask @seandavi to create an Orchestra environment with your current Docker image bhuvad/genesetanalysisworkflow for the time being.

[Gene233]

@Gene233 Thank you for the information. I can understand your situation. I don't think it's a problem if there is an update later. So I ask @seandavi to create an Orchestra environment with your current Docker image bhuvad/genesetanalysisworkflow for the time being.

Thanks! I'll update you when we finish the final changes.

[kozo2]

@Gene233 If you get errors like the attached image in the RStudio in your workshop Orchestra, uncheck the checkbox in the another attached image. The errors seem to come out when non-English is included in Rmd.

[Gene233]

@Gene233 If you get errors like the attached image in the RStudio in your workshop Orchestra, uncheck the checkbox in the another attached image. The errors seem to come out when non-English is included in Rmd.

Thanks! I'll check it later!