Scientists Map the Human Metabolome 39
Cache22x writes "Scientists at the University of Alberta have published the first draft of the Human Metabolome Project, the chemical equivalent of the human genome. In the same spirit as the human genome project, the information has been made freely available to the scientific community and the general public through the project's website. Knowing the makeup of the metabolome will lead to potentially enormous medical advances as clinicians now have a comparative base for analyzing the metabolite levels found in our bodies."
I don't get it (Score:3, Insightful)
Sing it with me fellas... (Score:1, Funny)
Re:I don't get it (Score:4, Informative)
That being said, I'm sure this could be a useful resource, and to be fair, it may actually be a little more appropriate to use "-ome" (which AFAIK basically means "the names of things") for a catalog like this than for the current state of the human genome, which is still basically a bunch of sequence data with a lot of significant sites, genes and otherwise, unidentified. My work deals with microarray analysis and statistical genetics; having worked with data from E. coli, mice, cattle, and people, I think it's reasonable to say we have "decoded the E. coli genome" but we're a long way from that with any eukaryote, including all mammals. And even with prokaryotes, we're a long way from really knowing everything that's going on -- job security, woo-hoo!
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Yes, it's almost c-omic. Bring back "-isms" and "-istics", I say!
Re:I don't get it (Score:4, Informative)
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boloyou! (Score:1)
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Re:boloyou! (Score:5, Funny)
Summary title a little misleading (Score:2, Informative)
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2) The OP's point is entirely correct, semantic nitpicking or no.
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Hmmm (Score:4, Informative)
Metabolome[1] refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signalling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method (see metabolomics). In January 2007 scientists at the University of Alberta finished a draft of the human metabolome. They have catalogued and characterized 2,500 metabolites, 1,200 drugs and 3,500 food components that can be found in the human body.
However, I am still in the dark about why this is required.
I suppose its like organising your stamp collection by number of nobbles around the edge.
Why it's important (Score:5, Informative)
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It's a big puzzle this, so we should be happy for every piece we get in place (:
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Metabolome (Score:4, Funny)
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DRM time! (Score:1, Funny)
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With genetic sequences being patented, are you really sure you aren't infringing on anyone's patent already?
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Heh. A good way to ensure that none of your genes are copied, is to stay in your mom's basement. Why even bother with DRM?
Males vs. Females (Score:2, Interesting)
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This may actually be more useful (Score:1, Interesting)
An explanation in computer terms (Score:5, Informative)
Okay, let me explain for you non-biochemist computer guys what this means. Take a computer, break it down into the smallest possible parts you can. I'm not talking about the hard drive/motherboard/case level. I'm talking about the level of transistors, resistors, ICs, connectors, motors, and the little blue LED that blinks whenever your hard drive spins. Now catalog everything. Keep a record of what you found where, and how many you found (eg, you found a laser in the DVD drive but not in the motherboard). So now you have a parts list, and a good idea of what parts to expect where. If you start finding unexpected things in unexpected places (like a SCSI connector on your video card, or an audio out port on one of your DIMMs), that tells you something is wrong.
Take a look at the database entry for something common like glucose [www.hmdb.ca]. It's got
Now what's missing is a lot of information about the connections, so technically this isn't really a map (because it's missing relational data), but a catalog. We need to know how each chemical turns into another, and what does the conversion. It's kinda like having a complete parts list for the computer, but not knowing how most of the parts fit together, nor how many volts and amps to run through the wires. Some of these connections we already know. I have a very large poster [expasy.org] on my wall illustrating the more common chemical pathways in various organisms. It's not nearly as complete as this catalog in terms of chemicals, but it's got a lot of connections.
The connections are what's really useful. To continue the computer analogy, if you know that the blue LED connects to the hard drive, then if you don't see the blue light blink, then there's probably something wrong with the hard drive. A significant number of drugs aren't active in the form that you take them. They become active when the body (usually in the liver) converts them from the delivery form to the active form. But some people, because of their genetic makeup, convert the drugs differently. They turn them into different metabolites. These metabolites might be totally inactive, or even toxic in some cases. So if you know the connecting system, you can put a drug in, look for what metabolites result, and determine whether or not that person should continue taking the drug.
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It is not parts. It is extracellular fluid systems (blood, urine, lymph). Continuing the computer analogy this would be: we know that there are diods inside the motherboard, but we can count only LEDs that are on the display panel. There is a relationship of course, but it still won't help you to see intracellular concentrations.
I see it much more as a medical tool (when they will be able to
A new age (Score:2)
step in the right direction! (Score:3, Insightful)
i didn't know about this database till now, so i played around alittle bit and find it usefull, but quite hard to use. the problem is more a technical one. if you for example open the entry of biotin here
http://www.hmdb.ca/scripts/show_card.cgi?METABOCA
you see a huge list of nice links that would maybe interest you (PDB, PubChem, KEGG,...) but there is a quite confusing part of such an entry (that's why i have choosen biotin as example, it is quite well known and a big entry) and that is the overview of the node itself related to the enzymes that make, degrade and modify the node. just listening the pathway names, the kegg maps and the SimCell maps, it may contain all the information needed, but it is not at all userfriendly, if you want to browse the metabolome and go from one node to another somewhere completely different... like you wolud be able to do on the big poster one tends to have. of course, the poster is missing a whole lot of information you have in a digital database, but it is much more userfriendly. you can use your finger to follow pathways
of course the enthusiastic biochemists among us would say, that we already have learned this overview in the textbooks and that you should know them by heart anyway.. but for natures (like me) who are more interested interdisciplinary and want to use this database as a browsable map.
some coding experts should sit together with the biologists to code a clickable SVG rendering map for a visual tour trough the metabolome
http://www.genome.jp/kegg/pathway/map/map00010.ht
but in a more interactive and more modern way (modern way = vector based, clickable, popups presenting links to other DBs and maybe adding color... or am i asking too much? *smile*).
great work - right step in the right direction!
You're Right!!!! (Score:2, Funny)
How to determine the metabolome: (Score:2)
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One of the lowest posting rates ever! (Score:2)
I can only conclude one of two things;
a) Nobody cares about "Canadian Science", unless it is Beer Science.
b) Nobody on Slashdot cares about biological stuff. They only care about stuff stuff.