Thread:Pathway is very simplified (2) - Revision history

Evelo at 22:37, 26 March 2020

Evelo — Thu, 26 Mar 2020 22:37:33 GMT

←Older revision		Revision as of 22:37, 26 March 2020
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	1) The paper Figure 5 seems to start from the virus itself and that crossing the membrane and interacting with cPLA2. after crossing through the glycerophospholipids bilayer. In this pathway, is seems to start with the glycerophospholipids themselves. Is that correct?		1) The paper Figure 5 seems to start from the virus itself and that crossing the membrane and interacting with cPLA2. after crossing through the glycerophospholipids bilayer. In this pathway, is seems to start with the glycerophospholipids themselves. Is that correct?

-	2) I think cPLA2 produces multiple fatty acids: palmitic acid, oleic acid and linoleic acid are the relevant ones here. They all come from the ellipsoid thing that is labeled as "fatty acids" (note we could do the same using the ChEBI term). So palmitic acid oleic acid are not side-products from the linoleic acid production I think. The current drawing suggests they are.	+	2) I think cPLA2 produces multiple fatty acids: palmitic acid, oleic acid, and linoleic acid are the relevant ones here. They all come from the ellipsoid thing that is labeled as "fatty acids" (note we could do the same using the ChEBI term). So palmitic acid oleic acid are not side-products from the linoleic acid production I think. The current drawing suggests they are.

	3) The part on the left hand of the figure that mentions PAF C-16 and LPCAT is missing. While PAF C-16 actually is affected in the original study. I am not even sure what these are. But it might be relevant to add them to be able to study virus interactions?		3) The part on the left hand of the figure that mentions PAF C-16 and LPCAT is missing. While PAF C-16 actually is affected in the original study. I am not even sure what these are. But it might be relevant to add them to be able to study virus interactions?

-	4) The original paper actually shows what the virus infection does with the metabolites, using red "up" arrows. I think it would be nice to show the virus effects somehow without interfering with use for analysis. ~~In fact, such~~ red arrows ~~might be~~ a ~~nice way~~ to do ~~that~~.	+	4) The original paper actually shows what the virus infection does with the metabolites, using red "up" arrows. I think it would be nice to show the virus effects somehow without interfering with use for analysis. I originally suggested to use the same red arrows, but that actually would interfere with use for data analysis. In the end, we should probably just have a generic pathway and discuss how it was used in the description. I am also going to suggest a title change. Please revert if you do not agree.

Evelo at 14:46, 26 March 2020

Evelo — Thu, 26 Mar 2020 14:46:34 GMT

←Older revision		Revision as of 14:46, 26 March 2020
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-	Hi, we can extend it the make it more accurate in ~~anyway~~ we like. The pathway figure is a starting point.	+	Hi, we can extend it the make it more accurate in any way we like. The pathway figure is a starting point.
		+
		+	I have some questions after looking at the original virus-related paper:
		+
		+	1) The paper Figure 5 seems to start from the virus itself and that crossing the membrane and interacting with cPLA2. after crossing through the glycerophospholipids bilayer. In this pathway, is seems to start with the glycerophospholipids themselves. Is that correct?
		+
		+	2) I think cPLA2 produces multiple fatty acids: palmitic acid, oleic acid and linoleic acid are the relevant ones here. They all come from the ellipsoid thing that is labeled as "fatty acids" (note we could do the same using the ChEBI term). So palmitic acid oleic acid are not side-products from the linoleic acid production I think. The current drawing suggests they are.
		+
		+	3) The part on the left hand of the figure that mentions PAF C-16 and LPCAT is missing. While PAF C-16 actually is affected in the original study. I am not even sure what these are. But it might be relevant to add them to be able to study virus interactions?
		+
		+	4) The original paper actually shows what the virus infection does with the metabolites, using red "up" arrows. I think it would be nice to show the virus effects somehow without interfering with use for analysis. In fact, such red arrows might be a nice way to do that.

Egonw: New page: Hi, we can extend it the make it more accurate in anyway we like. The pathway figure is a starting point.

Egonw — Thu, 26 Mar 2020 09:52:00 GMT

New page: Hi, we can extend it the make it more accurate in anyway we like. The pathway figure is a starting point.

New page

Hi, we can extend it the make it more accurate in anyway we like. The pathway figure is a starting point.