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|