Comparison of enrichment results with geneontology.org using ITAG4.1 GO annotation

[petemeng]

Hi Tobias,

Thank you for creating the ITAG4.1 GO annotation for tomato! This is a valuable resource for the plant research community.

I am currently using your annotation to perform GO enrichment analysis on my tomato RNA-seq data. I was wondering if you have compared the enrichment results obtained using your annotation (presumably with enrich() function in R) with the results obtained from the Gene Ontology Consortium website (https://www.geneontology.org/)?

Knowing if there are any discrepancies or inconsistencies between the two approaches would be helpful for interpreting my results. Thank you for your time and consideration.

Best regards,

[Tobias-deWerk]

Hi Peter,

I pulled the GO terms for ITAG4.1 directly from the solgenomics network (https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/annotation/ITAG4.1_release/) and simply converted GO:IDs to their descriptions for human readability. However, I discovered that the GO terms provided in ITAG4.1 (and 4.0 for that matter), are not of great quality. They contain many terms with sometimes 1 or 2 members, or outdated/synonymous terms.

If I'm not mistaken, geneontology.org uses SL3.00/ITAG3.0 genome release, which (I think) is why when you upload an (ITAG4.1) gene list, it will have a significant amount of unmapped IDs. I tried to create this script precisely to overcome that issue, but I can't fully attest to its quality.

Although they also use SL3.00, the release of ShinyGO (http://bioinformatics.sdstate.edu/go/) made this code a bit redundant.

Hope this helps!

Cheers, Tobias

[petemeng]

Hi Tobias,

Thank you for your quick reply and explanation. It is really helpful to understand the source and potential limitations of the ITAG4.1 GO annotation.

I agree with you that the quality of the current ITAG4.1 GO annotation seems to be suboptimal, especially considering the limited number of genes with associated GO terms. Having only slightly over 5,000 genes annotated out of the entire tomato genome significantly hinders comprehensive GO enrichment analyses.

Perhaps the community could benefit from a more comprehensive and updated GO annotation for ITAG4.1. It would be a significant contribution to enhance the accuracy and depth of functional analysis in tomato research.

Thank you again for your insights and for creating the current annotation.

Cheers, Peter

[Tobias-deWerk]

Hi Peter,

This is an insane coincidence (and indeed, I wish this was available one year ago), but I just stumbled across this, it seems others agreed and updated the GO annotation last month.

Gene ontology functional annotation datasets for the ITAG3.2 and ITAG4.0 tomato (Solanum lycopersicum) genome annotations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11033075/

Cheers, Tobias

[petemeng]

Hi Tobias,

Wow, that is an insane coincidence! Thanks so much for sharing this with me. I really appreciate it, and yes, having this a year ago would have been amazing! It's great to see others saw the need and updated the GO annotations.

I'll definitely check out the paper.

Best, Peter