Tag Archives: mitochondria

Video Tip of the Week: Mitochondrial transcriptome GBrowser

Subtitled: the data is not in the papers anymore. Again. And again.

As the data deluge continues, and those next-gen sequencing setups and labs continue to crank out more and more data, the details cannot be captured in the papers anymore. They just can’t. Authors can summarize the key findings, and show compelling examples and representative pieces. But they simply can’t show the volume of data that comprises the complete oeuvre from a given project anymore.

This is a point we keep hammering on. Knowing how to effectively use the software that stores and displays this data is now just as important as learning how to read publications in the first place. In the stone age when I was in grad school, most of what you needed to grasp from a paper was within the text and figures in the main body. Those days are gone in genomics, and they are never coming back. However, the software has limitations too. I’ll get to that later…

I was alerted to this interesting paper on Google+ by Robert West (but the specific item was unlinkable, sorry). The research involves analysis of the human mitochondrial transcriptome. Which even as a 1-off sort of assessment would have been interesting. But this group evaluated the transcriptome in over a dozen tissues and cell lines. That’s a lot of data.

And the paper summarizes key highlights–like the fact that the transcriptome does vary by tissue. Heart and muscle have different energy requirements and it appears to be reflected in their mitochondria at the level of transcript abundance. And there is a terrific Circos diagram (Figure 1) to summarize a lot of what they examined and mapped.

But: there’s no way for you to convey in a traditional publication all of those results. No. Way. And yes, I realize there are 6 large supplements attached to this paper. But that’s still not good enough.

I am delighted to report that there is a whole genome browser provided for a large fraction of this data: http://mitochondria.matticklab.com . That is da bomb, IMHO.

So in this week’s tip of the week will show you how to look at the data from this paper in the custom GBrowse that was built for this paper. We’ll have a look at how to display the tracks you want to explore.

As great as this special browser is, though, this paper made me aware of a limitation of this representation as well. The team of researchers was also interested in nuclear-encoded genes for mitochondrial proteins. Also intriguing to think about–because you can also imagine tissue-specific issues around nuclear gene expression impacting the functions of the mitochondria. But what you can’t do in this browser is layer that on. I mean, I can imagine a way to kludge that together, in fact. You could add those genes to one end of the linear representation, with some spacers, and sort of fake it out. Like this I mean pretend this is the reference sequence:

===nuclear gene1===nuclear gene2===nuclear gene3===mitochondrial genome===

And then you could compare them all together. But it’s certainly a work-around rather than a real complex visualization. We need better visualization tools. (I have a thought here that a custom Caleydo would work, but I’d be interested in other ideas too).

So that’s what I think, to summarize: the data’s not in the papers; you need to be as adept at software are you are at reading; and we need more and better visualization tools. But this was one cool example of all of that, plus a very cool and informative set of results. I’ve been thinking about this for a while since I read it. And those are my favorite papers–the ones that make me think about a whole bunch of different things.

Quick links:

Human mitochondrial transcriptome browser: http://mitochondria.matticklab.com

GBrowse: http://gmod.org/wiki/Gbrowse

Reference:
Mercer, T., Neph, S., Dinger, M., Crawford, J., Smith, M., Shearwood, A., Haugen, E., Bracken, C., Rackham, O., Stamatoyannopoulos, J., Filipovska, A., & Mattick, J. (2011). The Human Mitochondrial Transcriptome Cell, 146 (4), 645-658 DOI: 10.1016/j.cell.2011.06.051

Mito Much?

mitochondrion_186.jpgA recently sweep of the literature (courtesy of my standing My NCBI search) led me to another mitochondrial resource that I thought I would mention. MITOMASTER is the resource, and you can find details about it in this paper:

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences.

So of course I went to explore–I love a new database! Wandering around a bit, I find that they are the Molecular and Mitochondrial Medicine and Genetics Center (MAMMAG). I find this incredibly difficult to say–which is rather odd, since both my first and last name start with M you would think I would be better that this…

In any case, they are the home of a bunch of Mito features, it turns out. MitoMed, MitoMap, MitoWiki and MitoMaster. So I will now always think of it as the Mito4 place.

Mitomap is a database of human mitochondrial variations. You can access the existing site here: http://www.mitomap.org/ But it appears that they are planning a new version, and they are looking for input if you have some: http://mammag.web.uci.edu/twiki/bin/view/Mitomap/WebHome

The page had a number of links to other mito resources that were new to me–including the FBI Forensic mtDNA database. I have to admit, I went to peek at it to see what was in there. But it requires a download. I’m just not downloading stuff from the FBI….

You have to register to access part of the site, so I did. Then I tried out Mitomaster with a sequence I pulled out of GenBank. Quite a straighforward interface. It seemed to run fast and deliver interesting information about the variants. There was a button for each variant that quickly offered a more detailed look at any changes in a given gene. Seemed like a pretty useful option. I’ll try it out more soon–but I wanted to mention it while the paper was fresh in my mind.

MitoWheel

mitowheel.jpgAttilachordash at the blog Pimm – Partial immortalization points us to a tool for visualization of human mitochondrial genome sequence. You can use MitoWheel 1.2 to load and spin the genome around…kinda like a roulette wheel. Reportedly a game is coming soon. From the blog description:

MitoWheel is a graphical representation of the circular human mitochondrial genome, hence the name. The sequence used is the standard Revised Cambridge Reference Sequence. The 3 main components of the app is: a search box, a sequence bar and the wheel.

You can access MitoWheel here: http://mitowheel.org/mitowheel.html You can get the wheel spinning by clicking the arrowheads on the sequence line. I actually don’t know much else because the “how to use” is “under construction”. Your best bet is to check out the blog for more: http://mitowheel.wordpress.com. Especially if this is something you can use for your research, be sure to check out the update post about the newest features: MitoWheel 1.2: Humankind in the Wheel I think that means that there are nearly 3000 people in there now!

It isn’t something that expect to need to use, but I thought I would mention it for those who are interested in mtDNA. And it was kinda fun to spin it around….