Editing Transcriptome (section)

==Relation to other ome fields==
[[Image:Metabolomics schema.png|thumb|350px|General schema showing the relationships of the [[genome]], transcriptome, [[proteome]], and [[metabolome]] ([[lipidome]]).]]
Similar to other [[Omics|-ome]] based technologies, analysis of the transcriptome allows for an unbiased approach when validating hypotheses experimentally. This approach also allows for the discovery of novel mediators in signaling pathways.<ref name="cellerinopre">{{Harvnb|Cellerino|Sanguanini|2018|p=preface}}</ref> As with other -omics based technologies, the transcriptome can be analyzed within the scope of a [[multiomics]] approach. It is complementary to [[metabolomics]] but contrary to proteomics, a direct association between a transcript and [[metabolite]] cannot be established.

There are several -ome fields that can be seen as subcategories of the transcriptome. The [[exome]] differs from the transcriptome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities. Additionally, the transcritpome also differs from the [[translatome]], which is the set of RNAs undergoing translation.

The term meiome is used in [[functional genomics]] to describe the meiotic transcriptome or the set of RNA transcripts produced during the process of [[meiosis]].<ref>{{cite journal|title=Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat|journal=[[BMC Genomics]]|first1=Wayne|last1=Crismani|first2=Ute|last2=Baumann|first3=Tim|last3=Sutton|first4=Neil|last4=Shirley|first5=Tracie|last5=Webster|first6=German|last6=Spangenberg|first7=Peter|last7=Langridge|first8=Jason|last8=A Able|year = 2006|volume=7|issue=267|pages = 267|doi=10.1186/1471-2164-7-267|pmid=17052357|pmc = 1647286|doi-access=free}}</ref> Meiosis is a key feature of sexually reproducing [[eukaryote]]s, and involves the pairing of [[homologous chromosome]], synapse and recombination. Since meiosis in most organisms occurs in a short time period, meiotic transcript profiling is difficult due to the challenge of isolation (or enrichment) of meiotic cells ([[meiocyte]]s). As with transcriptome analyses, the meiome can be studied at a whole-genome level using large-scale transcriptomic techniques.<ref>{{cite journal|title=Whole genome approaches to identify early meiotic gene candidates in cereals|first1=William|last1=D. Bovill|first2=Priyanka|last2=Deveshwar|first3=Sanjay|last3=Kapoor|first4=Jason|last4=A. Able|doi=10.1007/s10142-008-0097-4|pmid=18836753|journal=Functional & Integrative Genomics|year=2009|volume=9|issue=2|pages = 219–29|s2cid=22854431}}</ref> The meiome has been well-characterized in mammal and yeast systems and somewhat less extensively characterized in plants.<ref>{{cite journal|title=Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice|journal=BMC Plant Biology|first1=Priyanka|last1=Deveshwar|first2=William|last2=D Bovill|first3=Rita|last3=Sharma|first4=Jason|last4=A Able|first5=Sanjay|last5=Kapoor|volume=11|issue=78|date=9 May 2011|pages=78|doi=10.1186/1471-2229-11-78|pmid=21554676|pmc=3112077 |doi-access=free }}</ref>

The [[thanatotranscriptome]] consists of all RNA transcripts that continue to be expressed or that start getting re-expressed in internal organs of a dead body 24–48 hours following death. Some genes include those that are inhibited after [[fetal development]]. If the thanatotranscriptome is related to the process of programmed cell death ([[apoptosis]]), it can be referred to as the apoptotic thanatotranscriptome. Analyses of the thanatotranscriptome are used in [[forensic medicine]].<ref>{{cite journal|last1=Javan|first1=G. T.|last2=Can|first2=I.|last3=Finley|first3=S. J.|last4=Soni|first4=S|year=2015|title=The apoptotic thanatotranscriptome associated with the liver of cadavers|journal=Forensic Science, Medicine, and Pathology|volume=11|issue=4|pages=509–516|doi=10.1007/s12024-015-9704-6|pmid=26318598|s2cid=21583165}}</ref>

[[Expression quantitative trait loci|eQTL]] mapping can be used to complement genomics with transcriptomics; genetic variants at DNA level and gene expression measures at RNA level.<ref>{{cite journal|title=Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences|first1=Claudia|last1=Manzoni|first2=Demis|last2=A Kia|first3=Jana|last3=Vandrovcova|first4=John|last4=Hardy|first5=Nicholas|last5=W Wood|first6=Patrick|last6=A Lewis|first7=Raffaele|last7=Ferrari|journal=[[Briefings in Bioinformatics]]|volume=19|issue=2|date=March 2018|pages=286–302|doi=10.1093/bib/bbw114|pmid=27881428|pmc=6018996}}</ref>

===Relation to proteome===
{{Further|Proteome}}
The transcriptome can be seen as a subset of the [[proteome]], that is, the entire set of proteins expressed by a genome.

However, the analysis of relative mRNA expression levels can be complicated by the fact that relatively small changes in mRNA expression can produce large changes in the total amount of the corresponding protein present in the cell. One analysis method, known as [[gene set enrichment analysis]], identifies coregulated gene networks rather than individual genes that are up- or down-regulated in different cell populations.{{ref|Subramanian}}

Although microarray studies can reveal the relative amounts of different mRNAs in the cell, levels of mRNA are not directly proportional to the expression level of the [[protein]]s they code for.<ref>{{cite journal |last=Schwanhäusser |first=Björn |journal=Nature |volume=473 |issue=7347 |pages=337–342 |pmid=21593866 |doi=10.1038/nature10098 |title=Global quantification of mammalian gene expression control |date=May 2011|bibcode=2011Natur.473..337S |s2cid=205224972 |display-authors=etal|url=http://edoc.mdc-berlin.de/11664/1/11664oa.pdf }}</ref> The number of protein molecules synthesized using a given mRNA molecule as a template is highly dependent on translation-initiation features of the mRNA sequence; in particular, the ability of the translation initiation sequence is a key determinant in the recruiting of [[ribosome]]s for protein [[translation (genetics)|translation]].