I haven’t looked into vitamin B6 in before and just looked at the Wikipedia article today. I start with general things:
A lot of what happens with metabolic pathways well modeled with control theory.
The body has an “idea” of how much it needs of a given substance and then up and downregulates genes to get to the targeted amount.
It’s possible that the presence of a vitamin activates a gene that then produces an enzyme that process the vitamin.
It’s possible that the presence of the vitamin blocks a gene that produces an enzyme that produces the vitamin or helps making the vitamin available from food.
In addition to regulation like that where the effects are immediate, methylation also allows the body to switch off genes for longer amounts of time.
To look at Vitamin B6 in particular you get https://www.genome.jp/kegg-bin/show_pathway?map00750 as a map of the related process and genes. It’s possible that some of them are not expressed because they get methylized when they aren’t needed.
If you want to go deeper into the topic, learn what the things in the pathway happen to be and what we already know about how the related genes are regulated. You can search through existing papers for everything involved.
If some of the involved parts of the pathway don’t have Wikipedia pages, the task of writing a Wikipedia page about them to explain what information there is about them is a useful way to study them.
There are a lot of different genes and there’s more reserach interest in some of them then others. If you can summarize on Wikipedia what a gene does for which there currently isn’t that much research interest you might produce an article that’s useful for anyone who cares in the future about knowing what the gene is about.
The KEGG reference here is good. Thank you! I’m hoping to get to a point where I could take something like what’s in KEGG and kind of play with it? Like if you’ve used something like Emergent to model the brain, something like that but with metabolic pathways.
Like take a set of metabolic pathways, play with amounts of chemicals, enzymes, genes that are and aren’t expressed, etc and use it run a simulation and test hypotheses? Would like to see what ways I could get pyridoxine, pyridoxal, pyridoxamine, etc to “build up.”
Like take all the edges and vertices and say “I’m increasing the amount of the chemical represented by this vertex at this rate and then then changing the rate at which it moves to this edge through this these other vertices and what happens if I do that?”
I know there’s a lot of software listed for that, and I could just start trying all of it. But I’m hoping to see if I can get something of a head start from someone that’s already familiar with this space.
I haven’t looked into vitamin B6 in before and just looked at the Wikipedia article today. I start with general things:
A lot of what happens with metabolic pathways well modeled with control theory.
The body has an “idea” of how much it needs of a given substance and then up and downregulates genes to get to the targeted amount.
It’s possible that the presence of a vitamin activates a gene that then produces an enzyme that process the vitamin.
It’s possible that the presence of the vitamin blocks a gene that produces an enzyme that produces the vitamin or helps making the vitamin available from food.
In addition to regulation like that where the effects are immediate, methylation also allows the body to switch off genes for longer amounts of time.
To look at Vitamin B6 in particular you get https://www.genome.jp/kegg-bin/show_pathway?map00750 as a map of the related process and genes. It’s possible that some of them are not expressed because they get methylized when they aren’t needed.
If you want to go deeper into the topic, learn what the things in the pathway happen to be and what we already know about how the related genes are regulated. You can search through existing papers for everything involved.
If some of the involved parts of the pathway don’t have Wikipedia pages, the task of writing a Wikipedia page about them to explain what information there is about them is a useful way to study them.
There are a lot of different genes and there’s more reserach interest in some of them then others. If you can summarize on Wikipedia what a gene does for which there currently isn’t that much research interest you might produce an article that’s useful for anyone who cares in the future about knowing what the gene is about.
The KEGG reference here is good. Thank you! I’m hoping to get to a point where I could take something like what’s in KEGG and kind of play with it? Like if you’ve used something like Emergent to model the brain, something like that but with metabolic pathways.
Like take a set of metabolic pathways, play with amounts of chemicals, enzymes, genes that are and aren’t expressed, etc and use it run a simulation and test hypotheses? Would like to see what ways I could get pyridoxine, pyridoxal, pyridoxamine, etc to “build up.”
Like take all the edges and vertices and say “I’m increasing the amount of the chemical represented by this vertex at this rate and then then changing the rate at which it moves to this edge through this these other vertices and what happens if I do that?”
I know there’s a lot of software listed for that, and I could just start trying all of it. But I’m hoping to see if I can get something of a head start from someone that’s already familiar with this space.