Hi Juliana, nice presentation with figures. What is the function for AT4G32060 in leaf? Because same AS is happening in all different drought condition, are AS in these examples keys for protein synthesis?
For AT4G32060, it functions as a negative regulator of mitochondrial calcium uptake. These same AS happened in all drought condition, might define as the the adaptation for drought condition.
Hi Juliana. Great presentation, very clearly delivered with nice figures and sequence highlighting.
In each comparison result, you seem to have highlighted one significant gene. Were these the sole results of each analysis, or were they the “top hits” out of a list of significant genes? If you looked at all significant genes, what was the method used to determine the cutoff for significance?
For the examples, they are the top hits from the comparison, and I picked the ones that can be visualized by graph the best. I tried to look at all significant genes, from the table the comparison command returns, it also includes a percent of sequence inclusion. I sorted the differences between two groups’ PSI; unfortunately, the result is not good enough. For some AS event, it will happen in all replicate, except for one, then the difference will be large too, but it’s not a significant AS event.
Hi Julianna, interesting results. I noticed you only included one AS event in your creation of your alternative transcripts for a particular gene. Have you thought about the multiple combination of AS events ? How could you verify all the different combinations experimentally?
From the table returned, it only included one AS in each AS event. I believe there must have some combination of AS events, where have IR and EX in same gene. To verify the combination experimentally, need to alter the gene of the protein, and see if the combinations cause any differences.
Hello Juliana, I have watched the second presentation. Nice presentation and great introduction to the eFP browser and ePlant! You made it easy to understand with the animated arrows. The DNA view for visualizing SOG1, a regulator of DNA damage response, is a cool add-on to the Tissue and Experiment Viewer. I wonder how were the SVG images for the DNA strands created? And why did you chose SVG over other files types such as PNG/ JPEG? Currently, are there any blooming plant species containing relevant experimental data in DNA damage response that the corresponding ePlant can implement the DNA image view other than Arabidopsis? Thank you!
Hi Juliana, nice presentation with figures. What is the function for AT4G32060 in leaf? Because same AS is happening in all different drought condition, are AS in these examples keys for protein synthesis?
Hi, Wen Kai,
For AT4G32060, it functions as a negative regulator of mitochondrial calcium uptake. These same AS happened in all drought condition, might define as the the adaptation for drought condition.
Hi Juliana. Great presentation, very clearly delivered with nice figures and sequence highlighting.
In each comparison result, you seem to have highlighted one significant gene. Were these the sole results of each analysis, or were they the “top hits” out of a list of significant genes? If you looked at all significant genes, what was the method used to determine the cutoff for significance?
Hi, Luke
For the examples, they are the top hits from the comparison, and I picked the ones that can be visualized by graph the best. I tried to look at all significant genes, from the table the comparison command returns, it also includes a percent of sequence inclusion. I sorted the differences between two groups’ PSI; unfortunately, the result is not good enough. For some AS event, it will happen in all replicate, except for one, then the difference will be large too, but it’s not a significant AS event.
Hi Julianna, interesting results. I noticed you only included one AS event in your creation of your alternative transcripts for a particular gene. Have you thought about the multiple combination of AS events ? How could you verify all the different combinations experimentally?
Hi, Vince
From the table returned, it only included one AS in each AS event. I believe there must have some combination of AS events, where have IR and EX in same gene. To verify the combination experimentally, need to alter the gene of the protein, and see if the combinations cause any differences.
Hello Juliana, I have watched the second presentation. Nice presentation and great introduction to the eFP browser and ePlant! You made it easy to understand with the animated arrows. The DNA view for visualizing SOG1, a regulator of DNA damage response, is a cool add-on to the Tissue and Experiment Viewer. I wonder how were the SVG images for the DNA strands created? And why did you chose SVG over other files types such as PNG/ JPEG? Currently, are there any blooming plant species containing relevant experimental data in DNA damage response that the corresponding ePlant can implement the DNA image view other than Arabidopsis? Thank you!