Abstract
In genome-scale datasets, Gene Ontology (GO) enrichment is a common analysis to highlight functions over-represented or under-represented in a subset of differentially expressed genes to elucidate the biological significance of the results. However, despite the diversity of existing tools to analyze GO enrichment, it is often difficult to integrate results in an article figure with sufficient clarity. This is partly due to the high number and to the redundancy of the enriched GO terms, especially when looking at large sets of differentially expressed genes. Here, we provide a simple method to plot representative enriched GO terms. The list of representative enriched GO terms is obtained using existing tools Panther and REVIGO and results are represented in different plots generated from a homemade R script and the ggplot2 R package. The generated plots are publication-quality figures. The diversity of represented parameters makes the plots highly informative (number of genes associated with the enriched GO terms, fold enrichment and level of statistical significance). Comparison of GO enrichment between different lists of genes in a single plot is possible. As proof of concept, we performed this analysis on an Arabidopsis heat responsive transcriptome dataset recently published.
Keywords: Omics data, Transcriptomics, Gene Ontology Enrichment, Biological Processes, R plot, ggplot2
Materials and Reagents
Equipment
Software
Procedure
Notes
In the R script, text preceded with ‘#’ should be considered as user notes, it will not be read by the computer if the whole script is copied and pasted into the R or macro consoles.
Acknowledgments
We would like to thank members from the Nagel and Bailey-Serres lab for helpful comments and suggestions to improve the functionality of this method.
Competing interests
The authors declare that there are no conflicts of interest or competing interests.
References
If you have any questions/comments about this protocol, you are highly recommended to post here. We will invite the authors of this protocol as well as some of its users to address your questions/comments. To make it easier for them to help you, you are encouraged to post your data including images for the troubleshooting.
It's ok. I can't open it with google chrome but it works with firefox.
Dear Clara,Thank you for your interest in our bio-protocol. Sorry to hear that you are having difficulty downloading the script. I just emailed you this file (Supplementary Data 3). Please let us know if you have any questions. Thanks,Titouan
Thanks for bringing this issue. The "Supplementary Data S3" is the script file for R (or RStudio). It's saved and uploaded here in a compressed file (.RAR format). You may need to extract the original script file first. Hope it helps with your question.
Thanks for your response. I know that this file is compressed but the problem is that the compressed file is corrupted and nothings can be extracted. I tried several times. If possible replace it with a corrected file or original script without compression. Regards
Supplementary Data S3 is not corrupted. That rar file needs to be converted into a zip folder (you can do it online if you don't have a converter)
Hello, Sorry to hear that you are having difficulties to download the files. As mentioned in the responses above, the Supplementary Data S3 is not corrupted and the problem probably comes from the conversion of the .rar file.Please don't hesitate to contact me at tbonnot@ucr.edu if you still have difficulties in accessing the files. I can directly send you these files. Thank you,Titouan Bonnot
Hello,It seems that some users get the following error message when running the R script "Supplementary Data 3":'Error: Guide with class guide / legend does not implement guide_transform(). Did you mean to use guide_axis()?'.It does not occur with everyone. If this happens to you, please remove from the R script (Supplementary Data 3) the code on lines 53 and 54 and remove the '+' at the end of the command 'labs(color="-log10(FDR)", size="Number\nof genes")+' on line 52. Remove the same code on lines 115 and 116 and the '+' on line 114 as well.We are currently in contact with the editorial team to provide an updated version of this Supplementary Data 3.We sincerely apologize for the inconvenience. Thank you,Titouan Bonnot