1. If we know gene1, gene2 are affecting the binding activity of TF1, are we allowed to use such information?
2. Some TFs are likely to co-bind. For example, if TF1 binds to region1, then there is a 60% probability that TF2 will bind to region1. Are we allowed to use such information?
Thanks,
Yichao
Created by yichao li unfashionable This is totally fine. The key point is that you are using gene expression levels we provided. How you selected which genes to use is totally upto you.
-Anshul. Hi Anshul,
I still need some clarifications.
1. We find Gene1 affects TF1 binding from the STRING database. I want to use the gene expression level of Gene1.
2. We find Gene2 affects TF1 binding from a paper (or experience). I want to use the gene expression level of Gene2.
Which one of them (or both) am I allowed to use for this challenge?
Thanks,
Yichao Yes. This should be fine.
Anshul Hi Anshul,
We have some biologists in our team. They know which genes are affecting TF1.
For (1), we're going to use the gene expression levels. I guess we can use this kind of information.
For (2), we're going to set a prior for TF co-binding.
We are not using any data types that are outside this challenge. But I guess we will use some information from the literature or experience.
So, overall, we are allowed to do this kind of thing because we are only using the data types within this challenge. Right?
Thanks,
Yichao Hi Yichao,
You need to clarify how you plan to use this information. E.g. For (1) if you wanted to use expression levels of gene1 and gene2, thats totally fine since you can use the provided gene expression in any way you want. E.g. For (2) you can use motifs of any cofactor TFs in your models as you like. The important thing is that you are only allowed to use the input and output data sets we provide (the exception being motifs/sequence affinity models - which you can derive or use from any external database/method). However, you are not allowed to use any other input data types directly in your models.
Let me know if that clarifies your question.
Thanks,
Anshul.