2021 Fiscal Year Research-status Report
Comprehensive optimization of cell type-specific gene co-expression networks and construction of a cell type-specific co-expression database
| Project/Area Number |
20K06609
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| Research Institution | Kyoto University |
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Principal Investigator |
VANDENBON ALEXIS 京都大学, ウイルス・再生医科学研究所, 准教授 (60570140)
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| Project Period (FY) |
2020-04-01 – 2023-03-31
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| Keywords | gene expression / gene co-expression / data normalization / database / batch effects / RNA-seq / network analysis |
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| Outline of Annual Research Achievements |
In fiscal year 2020-2021, I focused on the comprehensive analysis of different workflows for processing RNA-seq data into high-quality gene co-expression networks. In fiscal year 2021-2022, this comprehensive analysis was concluded, and the results of the analysis were published (Vandenbon, PLoS ONE, 2022).
The original analysis covered RNA-seq data from 68 human and 76 mouse cell types and tissues, on which I applied different RNA-seq normalization methods, different batch effect correction methods, and different measure of correlation. In brief, the results of the analysis showed that upper quartile normalization, followed by batch effect correction using a method called ComBat, and using Pearson correlation resulted in the best overall co-expression networks.
As part of the revision of the paper during the publication process, additional analyses were conducted to further support the findings of the study. For example, I confirmed the robustness of our findings, 1) using cross-validation, and 2) by changing parameters of the analysis. Our findings were confirmed to be robust. To improve the transparency and reproducibility, code used in the project was also made public on Github.
Finally, I implemented a first version of a gene co-expression database, in which a user can check the expression data of genes across the 68 human and 76 mouse cell types and tissues included in the dataset.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
In the original grant application, the plan of the project was as follows:
Part 1 (FY2020): focus on the collection of data, quality control of the data, and application of standard data processing steps. This was finished according to plan.
Part 2 (FY2020-FY2021): focus on the comprehensive evaluation of data normalization, batch effect removal, correlation measures, and network processing steps. Although I decided not to include network processing steps, the number of processing workflows was increased to 50 workflows, and this study was published (Vandenbon, PLoS ONE, 2022). In conclusion, this part too was finished according to plan.
Part 3 (FY2021-2022): focus on publication of results. Since I already published one paper about this project, I feel this project has advanced slightly faster than originally planned. In 2022 I will focus on the construction of a publicly accessible gene co-expression database.
On the other hand, my original plan included attendance of several domestic and overseas conferences to present this work to the scientific community. Due to the global pandemic, I have not been able to participate in such conferences.
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| Strategy for Future Research Activity |
I plan to finish the final part of the research plan. I will continue the construction of the gene co-expression database, and implementing its analysis tools. I will make the database accessible to the public scientific community, and hope to prepare a second paper which described the usage of the database.
In addition, I hope to be able to attend domestic and global conferences to present my work to the scientific community.
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| Causes of Carryover |
My original plan for this fiscal year included participation in 2 domestic and 1 overseas scientific conference to present my work. However, due to the global pandemic, I have not been able to participate in such conferences. As a result of that, I did not use the budget for domestic and overseas travel, nor conference registration fees, as originally planned.
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