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There’s no place like “ome”

Posted by Sandra Porter of Digital World Biology on December 1, 2006
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In which I present a quick guide for the omically challenged and a defense of ‘arth and “ome.”

Other SciBloggers have shared their thoughts on the use of ome here and here.

Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So many word pairs that once made phrases?;log in, data set, file name, set up, and pick up?;have been condensed into single words, that I’ve had to start using Google to double-check my editing. Perhaps it’s surprising then, that I like “ome,” “omics,” and even Sydney Brenner’s chief phrase-to-hate, “systems biology.”

I like “ome” because it simultaneously gives us more precise definitions for fields of study, while making a distinction between the reductionist view of biology, that was so popular when I was in graduate school, and the more global-omic-view that’s been emerging of late. When I grew up, we were mired in the one gene – one enzyme rut. We spent our time focused on single genes, single enzymes, single bands in gels, etc. It sounds funny now, but we actually questioned whether it made sense to sequence DNA if we didn’t know the function first.

Besides, “ome” sounds like “ribosome” and “spliceosome” and I’ve always liked those molecular machines, so why not head towards ome?

Whatever you think about ome, I’ve compiled a table of the omics I know of to help translate some of the old standby words into today’s omics.

Disclaimer: These are the definitions as I understand them, feel free to add suggestions and corrections in the comment section, if I like them I’ll add them to the table.

[updated 12/1/2006 thanks to Alex!]

[updated 12/2/2006 thanks to PhysioProf and the Atracinae spiders.]

[updated 12/3/2006 thanks to NicoR for the interactome, Hana for methylome and definition of the interactome, Bora for the time of omes, Lajos for a much more thorough omic collection (see the comments for the link).]

Ome & Field Definition Techniques Old word
Genome & Genomics All the genes in an organism. DNA sequencing, DNA assembly, BLAST, tools for translating open reading frames genetics
Comparative genomics Comparing genomes from different organisms BLAST, tools for drawing maps genetics
Structural genomics All the structures of molecules in an organism. X-ray diffraction, NMR biochemistry
Transcriptome All of the transcripts (RNA) produced by an organism Quantitative PCR, ESTs, microarrays, cDNA libraries genetics
Proteome & Proteomics All the proteins in an organism. 2D gels, mass spectroscopy biochemistry
Metabolome & Metabolomics All the biochemical pathways in an organism Enzyme assays biochemistry
Secretome All the molecules involved in secreting substances from a cell. 2D gels cell biology
Kinome All the molecules that can be phosphorylated, and the enzymes (kinases and phosphatases) that add or remove phospates. (is this last part correct?) 2D gels, radiolabelling cell biology
Glycome All the molecules that can be glycosylated, and the enzymes that carry out these reactions.   cell biology
Ubiquitome All the molecules that can be ubiquinated, and the enzymes that carry out these reactions. SDS-PAGE cell biology
Venome All the peptides in venom. 2D gels, mass spectroscopy zoology
Methylome, Methylomics? All the methylated bases in DNA (Does this should include RNA? RNA is often methylated, too). polyacrylamide gels biochemistry
Interactome All the proteins that touch each other. 2D gels, mass spectroscopy zoology
Chronome All the rhthyms, trends, and structures related to temporal changes in an organsism.   biology

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Comments

  1. #1 coturnix
    December 1, 2006

    In my written prelims back in 1999, I suggested that sooner or later there will be an organismome…until someone whispers that the term “physiology” already exists.

  2. #2 Sandra Porter
    December 1, 2006

    Sydney Brenner says that “systems biology” is physiology in disguise.

  3. #3 apalazzo
    December 1, 2006

    That’s it? How about kinome (all the kinases), ubiquitome (all the ubiquitinated proteins), phosphome (all the phosphorylated proteins) and glycome (all the glycosylated proteins). It’s getting ridiculous. To the point that I can’t take any new ‘omic coinage seriously …

    BTW “some” (as in ribosome, spliceosome, centrosome or even soma) comes from the greek word for “body” (soma=neuron cell body). Genome cames from the fusion of “gene” and “chromosome” (the later meaning colored body in greek – DNA can be stained with various dyes). I forgot who came up with that. But in light of this … what does the word metabolome have to do with a cell body???

  4. #4 apalazzo
    December 1, 2006

    cames = came (sorry ’bout that typo)

  5. #5 Sandra Porter
    December 1, 2006

    Alex: Thanks for the additions! I added them to the table – I’m still wondering if I can count the enzymes that add sugars as part of the glycome, ubiquitin as part of the ubquitome, kinases and phosphatases as part of the kinome, etc.

    If anyone knows, I do want the answer.

    Also – I think a “metabolome” could be the body of metabolic reactions that take place in a cell.

  6. #6 PhysioProf
    December 2, 2006

    We study the complex mixture of small peptides present in the venom of Atracinae spiders, the “venome”.

  7. #7 Sandra Porter
    December 2, 2006

    oooh, venome! I like it!

  8. #8 dileffante
    December 3, 2006

    This week Science titled a paragraph in their Editors’ Choice page with “Toward the Chaperome”… I first thought it was tongue in cheek, but apparently there is an organized community around the term (or an attempt at that). Time for the UN to coordinate some Ome non-proliferation effort.

  9. #9 NicoR
    December 3, 2006

    What about Marc Vidal’s interactome?

  10. #10 Hana
    December 3, 2006

    Other terms I’ve seen:

    - methylome (all the methylated regions of DNA in the genome) – interactome (the set of all protein-protein interactions in the cell)

  11. #11 coturnix
    December 3, 2006

    Here is chronome:

    Chronome n. The full complex of rhythms and temporal trends in an organism. The chronome consists of a multi-frequency spectrum of rhythms, trends, and residual structures, including intermodulations within and among physiological variables as well as changes with maturation and aging. // adj. = chronomic.

    You can do a Google or Google Scholar search to see how much it is actually used in the (human/medical) chronobiological literature. I was surprised myself! The term was coined by Franz Halberg, the same guy who coined the word “circadian”.

  12. #12 Lajos Incze
    December 3, 2006

    See a fuller list here: -Omes and -omics glossary. (Found in the wikipedia ‘-omics’ article.)

  13. #13 Sandra Porter
    December 3, 2006

    NicoR, Hana, Bora: Got it, I’ll add them.

    Lajos: Oh my goodness, I can’t keep with up typing all of those! Maybe I have to draw the line somewhere. CHI has practically taken a medical dictionary and added “ome” to everything! While terms like cardiogenomics – the genomics of heart cells – make sense to me, I’m kind of overwhelmed by it all. Maybe it’s time to play some Enya on my iPod, burn some incense, and sit cross-legged on the floor chant “ome” over and over again until my head stops threatening to explode. ; )

  14. #14 Sandra Porter
    December 3, 2006

    Lajos: Never mind, chanting “ome” doesn’t work for me. The dog seems to think there’s something wrong and keeps trying to lick my face.

  15. #15 coturnix
    December 3, 2006

    Wow, that’s a huge list….and no organismome?!

  16. #16 apalazzo
    December 4, 2006

    “is this last part correct?”

    I think that the kinome is usually restricted to all the kinases and phosphatases.

  17. #17 David Ng
    December 5, 2006

    You might like this piece at the SCQ: called “Like, “Omic” God!” (http://www.scq.ubc.ca/?p=114)

  18. #18 Sandra Porter
    December 5, 2006

    Thanks Alex!

    David: I do like it! thanks! I can’t believe I forgot to include pharmacogenomics!