Binding Sites
So it looks like I get to play the biologist today. I am going to try and figure out an easy way to get upstream and downstream sequences for a shopping list of genes. Then my colleague will see how likely our favorite transcription factor is to bind to each gene, either upstream or downstream. It seems pretty straightforward, but I have two worries. On my part, I’m not sure how easy it will be to get upstream or downstream regions for a collection of genes automated in bulk, not one at a time, and I’m not sure how far up or down to go in the intergenic region. 1kb? 2?
But after that, I’m not sure how reliable/usable our results will be, since our favorite transcription factor potentially interacts with lots of friends. Just because we determine it highly likely to bind upstream of some gene doesn’t mean it is not working in tandem with other transcription factors on some other gene, and we could miss that.
So far my biggest inhibitor of progress, at least as far as I can gauge from my mentor, is my dislike for trying things I doubt. For example, I am more likely to spend my time convincing myself that an undertaking (such as finding these 5′ and 3′ regions and binding sites) is worth the effort (and thus not making progress) than I am to try it and fail. I think some of that stems from my anxiety about finishing this degree in under a decade–I don’t want to waste time, per se. However, I guess you don’t learn unless you screw things up all the time, and I think I spend too much time avoiding mistakes than achieving success.
