I'm relatively new to building shiny apps, so any comments and suggestions would be greatly appreciated!
You can open a ticket on github or send me an email: l.jo@uu.nl
Thanks for the help!

It's really raw, but I would like to ask people to try this out on their own ggPlantmaps to see potential errors that can occur.
A link for the beta test instructions:
github.com/leonardojo/g...

Thanks!! I reposted it!

Thanks!!!!

I'll be happy to try something out if you have already a sample file! Let me know if you have something in mind!
All the best!

Hello Javier,
It would be super nice to have an automated tool, but finding one-fit-all segmentation tool would be really challenging. What I wanted to try is to check the output file of different automated tracing tools (microscopic, leaf shape,etc) and check how to convert them into a ggplot map.

This work was co-authored with Julie Pelletier, and concludes the main works I've done during my PhD in John's lab! We hope that this data is useful for people! Let me know if you have comments or suggestions, I'll be happy to address them.

GmWRI1 and GmLEC1 target each other in a positive forward loop to promote FA biosynthesis in seeds. We explored a bit the relationship between these two "master" regulators of seed lipid biosynthesis.

In a transient expression system, we evaluated the function of each motif in GmWRI1 binding sites. To our surprise, mutations in the AW-Box not always resulted in the reduction of enhancer activity, and mutations in the CNC-Box affected the transactivation of CAC2 by GmWRI1.

To further confirm these results, we identified the list of downregulated genes in the Arabidopsis wri1 mutants and upregulated genes by overexpressing GmWRI1 and identified that indeed, both AW-Box and CNC-Box to be enriched in regions downstream the TSS in Arabidopsis as well.

Motif analysis revealed the presence and enrichment of the AW-Box in WRI1 binding sites. It has been shown that this element is bound by WRI1 in vitro. Interestingly we found the presence of another element that we called CNC-Box (CNCCNCC).

When looking at the binding pattern of WRI1, we found that this TF binds preferentially at regions downstream the TSS. This pattern is different from other TFs we studied in the past (LEC1). What could be mechanistic and evolution relevance of this binding pattern?

After many failed attempts, we finally obtained a good GmWRI1 antibody that allowed us to perform a ChIP-Seq that passed ENCODE QC. With this dataset identified the list of potential target genes of GmWRI1 As expected, these genes encoded for many lipid related genes in seeds.