Last time we left off with looking at the Tabular view of the printing families order and manipulating the results by using words or protein family IDs. And also looking at the different ways you can filter down to different protein families. We also demonstrated how you could click on a single row and generate a multiple sequence alignment. But now, I want to leave the Tabular view and let's click up here on the Heatmap view. Okay, let's talk a little bit about what these colors mean. The sliders here I can pull it open and I can pull it open here, and then you can see more distinctly what the genomes are down the side and the protein families on the x-axis. So when a particular cell is black, and notice when I mouse over that celll, it gives me the information about the genome, the protein families, and how many proteins this particular genome has in this family. So when it's black, it means that this gene has not been annotated in this genome. When it's yellow, it means that this particular genome has one protein in this protein family. When it's this mustardy color or light orange color, it means that this particular genome has two proteins in this particular family. And when it's this bright orange, it means that it has three or more, note in the little pop up window, this particular genome, which is strain 9-941, has six proteins that belong to this protein family that is immobile element protein. So that's what the colors mean. Let's stretch down and stretch over so we can see all the real estate here and I wanted to talk about some of the functionality of this. You can scroll down and you can see different patterns within the protein families. In the next video, we're going to talk about manipulating this more, but this one's more about talking about these functions. I can flip the access if I like, I personally like this one because it has more real estate. I can grab particular genomes and move them around where I might want them to be, so see you could always up here now. So this is a great thing if you've done a phylogenetic tree in, there's an area that you want to show. Next to that, you could arrange the genomes depending the way they are arranged in the tree and then make a figure of that, that would be pretty sweet. You can search for things. Earlier we looked for flagella. And so look, I've got it here, and I'm just having it highlight where the protein families are that have that in the names, so that's showing it that way. You can see here is a cluster of protein families here that have flagella in the name. Or what we've used before is this keyword function, I'll let me clear the filter here. I can go in and I can still use the filter here. Like remember when we got all the protein families that the unique identifiers that corresponded to the O antigen genes. And then I can say I want to filter the heatmap based on that. And then we see only those protein families, and it's pretty clear here when you see things that have a problem that are missing genes in a particular protein family. And so that's one of the ways that you can manipulate the protein family. And you can reset it here and go back to normal. In our next video, we're going to show you how to do clustering. Thanks for listening and thank you for using Patrick, bye. In the last assignment, we had to use the filter on the table. Now, I want you to launch the Heatmap view and we're going to use the filter on the Heatmap. Let's first look at the heatmap, and over the heatmap is the text box. In the last assignment, I had to use the dynamic filter on the right and enter the word kinase in that filter, to see how it changed the table. In this one, in that text box, over the heatmap, enter the word kinase there and then filter on it. What happens to the heatmap? How does it change? And after you're finished with that, clear that filter. Then in the text box on the left I want you to enter kinase in there and filter it. This time, how does the heatmap change? Reset the filter. Now, just for fun, a lot of proteins that have metabolic functions and often pathways associated with them have the term EC for Enzyme Commission on them. And I want you to show that you can filter just on something as easy as two letters. So go ahead and put EC in the text box over the heatmap and filter it, and you could also do it on the dynamic filter to the left of the heatmap. Good luck and don't close that tab because we probably have more to do.
