Identifying Active and Alternative Promoters from RNA-Seq data with proActiv (original) (raw)

Summary

Most human genes have multiple promoters that control the expression of distinct isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases.

proActiv is a method that enables the analysis of promoters from RNA-Seq data. proActiv uses aligned reads as input, and then generates counts and normalized promoter activity estimates for each annotated promoter. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions.

Here we present a quick start guide to using proActiv, and a detailed workflow for identifying active promoters and alternative promoters across 2 conditions.

If you use proActiv in your research, please cite:

Demircioğlu, Deniz, et al. “A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.” Cell 178.6 (2019): 1465-1477.

Contents

• Quick Start: Quantifying promoter activity with proActiv
• A complete workflow to identify alternative promoter usage
  • Preparing input data
  • Preparing promoter annotations
  • Running proActiv
  • Identifying alternative promoters
• Analysis and visualization of alternative promoter usage
  • Alternative promoter usage
  • Promoter category proportion
  • Major/minor promoters by position
  • Major promoter activity and gene expression
  • t-SNE
• Getting help
• Citing proActiv
• Session information

Session information

#> R version 4.0.3 (2020-10-10)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19041)
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#> [3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C                      
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#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
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#> other attached packages:
#> [1] Rtsne_0.15     ggplot2_3.3.3  gridExtra_2.3  proActiv_1.3.3
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