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Scientists Map the Human Metabolome
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."
The metabolome hasn't been mapped like the genome has been mapped. i.e. it's not a complete list of metabolic reactions, enzymes and small molecules in a human cell.. it's a database (currently with 2100 metabolites) for the classic biochemical charts that show metabolism networks (like how the citric cycle is connected to amino-acid production). Nonetheless, it's a great idea, and as a BSc graduate from the dept, I'm quite proud.
Incase you don't know what it is (like I didn't, here is the wikipedia definition:
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.
liqbase
It doesn't. The "-ome" and "-omics" suffixes are being thrown around with reckless abandon these days; it's like businesses sticking "e-" on everything during the dot-com boom.
;)
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!
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
This complements the genome project. DNA codes are used ultimately to make proteins, enzymes (and other things). Proteins and enzymes are used for metabolic processes in the cell (and other things). In fact, having knowledge of the metabolome is more useful for pharmaceutical and health sciences research than knowledge of the genome. Moreover, these networks are quite complicated and contain many redundancies and inter-relationships, and compiling it in a database makes it easier to see these relationships. The human metabolome is most directly useful in developing pharmaceuticals, but the metabolome databases for other organisms would be very useful as well -- such as Saccharomyces cerevisiae (yeast) and Escherichia coli. For example, in my lab we grow 13C/15N-isotope labeled protein molecules with cloned genes in E. coli, and being able to search a metabolism network database would help us identify small molecules to feed bacteria to get specific labeling patterns.
I should have clarified a bit more, but this is truly a draft map of the human metabolome. The database catalogues not just the chemical data but also concentrations of the metabolites in specific disorders, as well as providing spectral data. The metabolome data actually is gigabytes. The idea is that a doctor can take a urine, blood, or CSF sample, and compare the concentrations of each metabolite in the given biofluid to the known concentrations for normal and abnormal patients available at the HMDB. Although you can't do this yet, making the data available to the scientific community might enable this type of diagnosis. Some would argue the medical implications will be just as great as that of the human genome project, while others argue it is insignificant. Only time will tell.
Yes, concentration information contains data on Male/Female when available (when literature specified it or if it was done in-house).
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. 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 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.
I am glad you rephrased that. All things -ome represents a collection, not a comparison to the human genome. Examples: genome - collection of genes in an organism, proteome - collection of proteins in an organism, interactome - collection of protein interactions in an organism. The metabolome is just as you described, a detailed view of concentrations of many metabolic enzymes, and chemicals. One of the many applications of this is for weight loss. Imagine examining overweight people as they lose weight and finding markers indicative of weight loss. Suddenly you could have a surrogate marker for weight loss to quickly identify successful or bogus methods of weight loss. This is a field getting much funding from big pharm for obvious reasons in our super-sized lifestyle.