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Hello,
My lab partners and I were wondering why there can be many aliases for a transcription factor. When using the Amazonia! database, we noticed that the different aliases for ARP-1 had different cell type expressions. Does that mean these aliases are completely different transcription factors? Also, we chose skin as our target cell type and all of its transcription factors were highly expressed in other cell types. Therefore, these factors are all not specific enough for skin. Will this affect our results to make our tissue of interest? Finally, for our project, we have to make a visual. For this specific project should we show an example of a graph on the Amazonia! database and explain how we used it? Or should we try to make a diagram that vividly shows how transcription factors can change one cell type into another cell type?
Thank you,
Clarissa, Joy, and Cayla
How direct reprogramming can turn one cell type into another
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- Project Question: In this project we are experimenting how transcription factors can be used to change one cell type to a different cell type through direct reprogramming.
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Re: How direct reprogramming can turn one cell type into ano
Hi Clarissa, Joy and Cayla,
Great questions! I'll do my best to answer, so let me know if you have any questions.
Does that mean these aliases are completely different transcription factors? No - an alias is just another name for the same item, like a nickname. The name is generally selected by the group of scientists that were working on it and often, discovered it. Sometimes one group names the protein from one species and another group names it in a different species and later it is discovered it is the same protein. This can happen with different researchers working on the same species, or in different systems, too.
Also, we chose skin as our target cell type and all of its transcription factors were highly expressed in other cell types. Therefore, these factors are all not specific enough for skin. Will this affect our results to make our tissue of interest? This can happen alot. But did you look at the combination of factors used for skin? I think the combination of all transcriptions factors for the skin is different than in any other tissue, even if the other tissues share SOME of the same transcription factors... BUT this doesn't have to be true for it to work. There are other factors that cause the cell to differentiate than just the transcription factor signature.
Finally, for our project, we have to make a visual. For this specific project should we show an example of a graph on the Amazonia! database and explain how we used it? Or should we try to make a diagram that vividly shows how transcription factors can change one cell type into another cell type? I think a good visual will tell the story you are showing with your data. If you want to show that a stem cell starts out, and is finally turned into a skin cell, you could draw the different cells (their morphology is different, right?) and show the steps in between (molecular method of transcription/translation) - that's your second suggestion
I like that one!
Good luck with your project!
Tonya
Great questions! I'll do my best to answer, so let me know if you have any questions.
Does that mean these aliases are completely different transcription factors? No - an alias is just another name for the same item, like a nickname. The name is generally selected by the group of scientists that were working on it and often, discovered it. Sometimes one group names the protein from one species and another group names it in a different species and later it is discovered it is the same protein. This can happen with different researchers working on the same species, or in different systems, too.
Also, we chose skin as our target cell type and all of its transcription factors were highly expressed in other cell types. Therefore, these factors are all not specific enough for skin. Will this affect our results to make our tissue of interest? This can happen alot. But did you look at the combination of factors used for skin? I think the combination of all transcriptions factors for the skin is different than in any other tissue, even if the other tissues share SOME of the same transcription factors... BUT this doesn't have to be true for it to work. There are other factors that cause the cell to differentiate than just the transcription factor signature.
Finally, for our project, we have to make a visual. For this specific project should we show an example of a graph on the Amazonia! database and explain how we used it? Or should we try to make a diagram that vividly shows how transcription factors can change one cell type into another cell type? I think a good visual will tell the story you are showing with your data. If you want to show that a stem cell starts out, and is finally turned into a skin cell, you could draw the different cells (their morphology is different, right?) and show the steps in between (molecular method of transcription/translation) - that's your second suggestion
I like that one!Good luck with your project!
Tonya