10 Replies to “Bruno’s Summative (BCB330 and BCB430)”
Hi Bruno! I think your slides were a clean summary of the work you did! However, for some reason I couldn’t view your video. Wishing you the best, Rachel
Thanks for the advice, I downloaded the video as you suggested! Your presentation was very clear and informative! My question is does the expression data for aGENT use RNA-seq or microarray data? Is there a way tell what type of data it is for the user in aGENT?
Nice explanation about the project. When clear the nodes, Is it possible to clear the pathway for irrelavent nodes? or thoes pathes are also important??
Do you mean in the max expression filter? Currently the nodes stay there, only greyed out, but it is trivial to make them disappear when they’re outside the filtered range, but this loses information when both the Venn filter and the expression filter are used at the same time, since you can’t see the network that those nodes belonged to.
For your max expression work, could you list a usecase(s) for this data (aside from AGENT) and also give us the link (or POST params) for others to use this API?
I wonder if it was you or Rachel who first used that GRN image (slide 7), or it was simply a coincidence ;).
Even though AGENT is built with only Arabidopsis GRNs at the moment, can you fore see the implications/benefits of overlaying two inter-species GRNs?
I’m glad you discussed visual mapping as it is a core concept in data visualization (may I recommend you a few books during this quarantine?).
Sorry about the audio – I only had a $10 desk mic at hand.
Another use-case for the max expression data could be for prediction of function of unknown genes for which we may have expression data – one could find the tissues and conditions at which their expression is most highly induced or reduced, which could help determine their function in the cell.
You should have access to the API on GitHub – I’ve added a README with examples of the endpoints and how to use them.
I think the image is just one of the first examples of a GRN that shows up if you Google it – I think I used the same one in one of the previous presentations.
Yes, overlaying inter-species GRNs could be useful in finding conserved GRN patterns, and even in deducing the regulation of genes for which we do not have GRNs in one species but do in the other. However, it would need to be able to properly detect orthologs.
Re: the books, sure, feel free to send me recommendations!
Hey Bruno! I really enjoyed your project presentation, the work you did is really interesting and seems like it could have a lot of value to researchers. I was wondering if there was anyway to download the GRN data, such as relevant nodes in certain expression conditions etc.
Hi Bruno! I think your slides were a clean summary of the work you did! However, for some reason I couldn’t view your video. Wishing you the best, Rachel
Hi Rachel – that’s odd, maybe you’d be able to download it from the Media Library in WordPress
Hi Bruno,
Thanks for the advice, I downloaded the video as you suggested! Your presentation was very clear and informative! My question is does the expression data for aGENT use RNA-seq or microarray data? Is there a way tell what type of data it is for the user in aGENT?
Nice explanation about the project. When clear the nodes, Is it possible to clear the pathway for irrelavent nodes? or thoes pathes are also important??
Do you mean in the max expression filter? Currently the nodes stay there, only greyed out, but it is trivial to make them disappear when they’re outside the filtered range, but this loses information when both the Venn filter and the expression filter are used at the same time, since you can’t see the network that those nodes belonged to.
Hi Bruno,
Good work, although your audio was very staticky.
For your max expression work, could you list a usecase(s) for this data (aside from AGENT) and also give us the link (or POST params) for others to use this API?
I wonder if it was you or Rachel who first used that GRN image (slide 7), or it was simply a coincidence ;).
Even though AGENT is built with only Arabidopsis GRNs at the moment, can you fore see the implications/benefits of overlaying two inter-species GRNs?
I’m glad you discussed visual mapping as it is a core concept in data visualization (may I recommend you a few books during this quarantine?).
Hi Vincent,
Sorry about the audio – I only had a $10 desk mic at hand.
Another use-case for the max expression data could be for prediction of function of unknown genes for which we may have expression data – one could find the tissues and conditions at which their expression is most highly induced or reduced, which could help determine their function in the cell.
You should have access to the API on GitHub – I’ve added a README with examples of the endpoints and how to use them.
I think the image is just one of the first examples of a GRN that shows up if you Google it – I think I used the same one in one of the previous presentations.
Yes, overlaying inter-species GRNs could be useful in finding conserved GRN patterns, and even in deducing the regulation of genes for which we do not have GRNs in one species but do in the other. However, it would need to be able to properly detect orthologs.
Re: the books, sure, feel free to send me recommendations!
Good explanation for your project. I really like the way you post your code and result, and explain them at the same time.
Hi Bruno. Good job building a database! Really impressed with everything you’ve done. (:
Hey Bruno! I really enjoyed your project presentation, the work you did is really interesting and seems like it could have a lot of value to researchers. I was wondering if there was anyway to download the GRN data, such as relevant nodes in certain expression conditions etc.
Thanks!
Sakshi