ORFeome
In molecular genetics, an ORFeome refers to the complete set of open reading frames (ORFs) in a genome. The term may also be used to describe a set of cloned ORFs.{{Cite book | last1 = Ohara | first1 = O. | chapter = ORFeome Cloning | doi = 10.1007/978-1-60761-232-2_1 | title = Reverse Chemical Genetics | series = Methods in Molecular Biology | volume = 577 | pages = 3–9 | year = 2009 | isbn = 978-1-60761-231-5 | pmid = 19718504 }} ORFs correspond to the protein coding sequences (CDS) of genes. ORFs can be found in genome sequences by computer programs such as GENSCAN and then amplified by PCR. While this is relatively trivial in bacteria the problem is non-trivial in eukaryotic genomes because of the presence of introns and exons as well as splice variants.
Use in research
The usage of complete ORFeomes reflects a new trend in biology that can be succinctly summarized as omics. ORFeomes are used for the study of protein-protein interactions,{{cite journal |vauthors=Titz B, Rajagopala SV, Goll J, Häuser R, McKevitt MT, Palzkill T, Uetz P |title=The binary protein interactome of Treponema pallidum--the syphilis spirochete |journal=PLOS ONE |volume=3 |issue=5 |pages=e2292 |year=2008 |pmid=18509523 |pmc=2386257 |doi=10.1371/journal.pone.0002292 |bibcode=2008PLoSO...3.2292T |editor1-last=Hall |editor1-first=Neil|doi-access=free }} {{open access}}{{cite journal |vauthors=Uetz P, Rajagopala SV, Dong YA, Haas J |title=From ORFeomes to protein interaction maps in viruses |journal=Genome Research |volume=14 |issue=10B |pages=2029–33 |date=Oct 2004 |pmid=15489322 |doi=10.1101/gr.2583304|doi-access=free }} protein microarrays, the study of antigens,{{cite journal |last1=McKevitt |first1=Matthew |last2=Brinkman |first2=Mary Beth |last3=McLoughlin |first3=Melanie |last4=Perez |first4=Carla |last5=Howell |first5=Jerrilyn K. |last6=Weinstock |first6=George M. |last7=Norris |first7=Steven J. |last8=Palzkill |first8=Timothy |date=2005-07-01 |title=Genome scale identification of Treponema pallidum antigens |journal=Infection and Immunity |volume=73 |issue=7 |pages=4445–4450 |doi=10.1128/IAI.73.7.4445-4450.2005 |issn=0019-9567 |pmc=1168556 |pmid=15972547}} and other fields of study.
Cloned ORFeomes
Complete ORF sets have been cloned for a number of organisms including Brucella melitensis,{{cite journal | vauthors = Viadas C, Rodríguez MC, García-Lobo JM, Sangari FJ, López-Goñi I | title = Construction and evaluation of an ORFeome-based Brucella whole-genome DNA microarray | journal = Microbial Pathogenesis | volume = 47 | issue = 4 | pages = 189–95 | date = Oct 2009 | pmid = 19524659 | doi = 10.1016/j.micpath.2009.06.002 }}
Chlamydia pneumoniae,{{cite journal | vauthors = Maier CJ, Maier RH, Virok DP, Maass M, Hintner H, Bauer JW, Onder K | title = Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae | journal = BMC Genomics | volume = 13 | pages = 632 | year = 2012 | pmid = 23157390 | pmc = 3534531 | doi = 10.1186/1471-2164-13-632 | doi-access = free }}
Escherichia coli,{{cite journal | vauthors = Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P | title = The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology | journal = BMC Genomics | volume = 11 | pages = 470 | year = 2010 | pmid = 20701780 | pmc = 3091666 | doi = 10.1186/1471-2164-11-470 | doi-access = free }}
Neisseria gonorrhoeae,{{cite journal | vauthors = Brettin T, Altherr MR, Du Y, Mason RM, Friedrich A, Potter L, Langford C, Keller TJ, Jens J, Howie H, Weyand NJ, Clary S, Prichard K, Wachocki S, Sodergren E, Dillard JP, Weinstock G, So M, Arvidson CG | title = Expression capable library for studies of Neisseria gonorrhoeae, version 1.0 | journal = BMC Microbiology | volume = 5 | pages = 50 | year = 2005 | pmid = 16137322 | pmc = 1236931 | doi = 10.1186/1471-2180-5-50 | doi-access = free }}
Pseudomonas aeruginosa,{{cite journal | vauthors = Labaer J, Qiu Q, Anumanthan A, Mar W, Zuo D, Murthy TV, Taycher H, Halleck A, Hainsworth E, Lory S, Brizuela L | title = The Pseudomonas aeruginosa PA01 gene collection | journal = Genome Research | volume = 14 | issue = 10B | pages = 2190–200 | date = Oct 2004 | pmid = 15489342 | pmc = 528936 | doi = 10.1101/gr.2482804 }} Schizosaccharomyces pombe,
and human herpesviruses{{cite journal | vauthors = Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J | title = Evolutionarily conserved herpesviral protein interaction networks | journal = PLOS Pathogens | volume = 5 | issue = 9 | pages = e1000570 | date = Sep 2009 | pmid = 19730696 | pmc = 2731838 | doi = 10.1371/journal.ppat.1000570 | editor1-last = Sun | editor1-first = Ren | doi-access = free }}
A partial human ORFeome has also been produced.{{cite journal | vauthors = Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M | title = hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes | journal = Genomics | volume = 89 | issue = 3 | pages = 307–15 | date = Mar 2007 | pmid = 17207965 | pmc = 4647941 | doi = 10.1016/j.ygeno.2006.11.012 }}http://horfdb.dfci.harvard.edu/ Human ORFeome 2011 Release