Talk:Transcriptome

More than just expression profiling

I think the study of transcriptome involves more than just profiling of expression, but also simple cataloging transcript species, as well as determining their transcript structure (start, end sites), splicing patterns, etc. --Huggie (talk) 06:25, 18 July 2011 (UTC)

From PNA/Biology

• Transcriptome -- this page is just a skeleton with lots of headings and little else. And while the word is a bit dubious, the other xxxome-pages (expressome!? regulatome? give me a break) referenced smack way too much of creative word games. In addition, I don't think the definition is the only one possible; I'm fairly sure transcriptome is used to refer to the set of transcribed sequences, i.e. all the different transcripts produced from a genome. Ketil 2004-11-04
  • Transcriptome is a legitimate, albeit annoying, term in biology and has a place in comparative studies of states (e.g. cancerous vs. 'normal' tissue) and other comparative measures. It's one of those 'omics explosion' terms. Courtland 2005-01-31
  • I spent some time collapsing the lists of links on the several omics pages by introducing the List of omics topics in biology page and cleaning up the several pages it references. I do wish the person(s) who had originally put these up had not been in such a hurry to dash them up then walk away ... or so it seems from my perspective. At the very least they should have been put in as stubbies ... hey, that's not a bad middle ground really. What do you think? Courtland 2005-01-31 (almost 02-01)

Not just mRNA

I think the term "transcriptome" refers to all RNA transcripts, not just messenger RNA. Searching for the term on Pubmed leads to several articles that specifically mention trying to figure what's all that non-coding RNA doing. See also Affymetrix's page on the topic at http://www.affymetrix.com/transcriptome/index.affx, and I guess they should know since that's why their products exist (tracking expression levels). In fact, reading the first paragraph it sounds like the original author intended to mean all RNA transcripts. The last paragraph directly references an article where antisense transcripts are part of the transcriptome. Unless someone objects in the next few days, I'll edit the page to correct this. -Lp 70.81.26.125 16:02, 1 September 2007 (UTC)

redirect from Transcriptomics

I would suggest that the redirect from Transcriptomics should actually lead to Expression profiling since that page puts its focus mostly on the analysis on mRNA expression profiles.--Oleginger (talk) 15:33, 14 August 2008 (UTC)

non-coding RNA is not part of the transcriptome

According to T.A.Brown in Genomes 3:

The transcriptome is the set of protein coding RNA (just m-RNA and pre-mRNA). A bit confusing is that trancription gives non-coding RNA as well as the transcriptome. The transcriptome is about 4% of all RNA.

The non-coding RNA is also called functional RNA is not translated into proteins. The most important types of functional RNA are: Ribosomal RNA (rRNA), Transfer RNA (tRNA), Small nuclear RNA (snRNA or U-RNA), Small nucleolar RNA (snoRNA), MicroRNA (miRNA) and short interfering RNA (siRNA)

So I think there are corrections to be made in the article: 1. transcriptome IS just protein coding RNA 2. all others than (pre)mRNA are NON-coding.

2010-04-12, Enschede The Netherlands

I would respectfully suggest that the honorable T.A.Brown is incorrect.--Paul (talk) 21:47, 13 April 2010 (UTC)

Honorable T A Brown here. I think the word ‘transcriptome’ was first used by Bert Vogelstein and Kenneth Kinzler in papers in Cell (88, 243) and Science (276, 1268) in 1997. They did not specify exactly what they meant but reading the papers it is pretty clear they were thinking about the mRNA component of the cell. I wrote the first edition of Genomes just after those papers came out so defined transcriptome as the ‘mRNA content of the cell’. Personally I think that is the most useful definition as it means that the transcriptome is the coding RNA and hence the part of the total cell RNA that specifies the proteome and through that the biochemical capability of the cell. But I’m not an RNA biologist and what is important is what people who study the transcriptome actually think the word means now. I’m not sure though if there is really agreement in the field - for example, a recent paper in Cell is called ‘Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP” (Hafner et al, Cell 141, 129, 2010). That title seems meaningless to me if microRNAs are a part of the transcriptome. Terry Brown. —Preceding unsigned comment added by 86.185.134.42 (talk) 14:48, 17 April 2010 (UTC)

Hi Hon. TA Brown. ;-) I'm basing my argument on the the word Transcriptome, that is Transcipt and -ome - in this context essentially meaning 'of the genome'. I don't see anything specific to protein coding genes there. Just because a few microarray users have been using the term to mean protein coding genes doesn't, IMHO, make it true. I haven't contributed text to this article but I think the existing definition is correct. Especially given that most transcriptome work is now shifting to using RNA-Seq. Which, depending on the sample prep., is unbiased regarding protein coding content.--Paul (talk) 20:33, 18 April 2010 (UTC)