%0 Journal Article %1 Rajagopala2010Escherichia %A Rajagopala, Seesandra %A Yamamoto, Natsuko %A Zweifel, Adrienne %A Nakamichi, Tomoko %A Huang, Hsi K. %A Rios, Jorge M. %A Koh, Jonathan F. %A Boorgula, Meher %A Fujita, Kazutoshi %A Suzuki, Ken I. %A Hu, James %A Wanner, Barry %A Mori, Hirotada %A Uetz, Peter %D 2010 %J BMC Genomics %K comparative-analysis ecoli %N 1 %P 470+ %R 10.1186/1471-2164-11-470 %T The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology %U http://dx.doi.org/10.1186/1471-2164-11-470 %V 11 %X BACKGROUND:Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion.RESULTS:We have constructed an open reading frame (ORFeome) collection of 3974 or 94\% of the known Escherichia coli K-12 ORFs in Gateway(R) entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this ORFeome with other Gateway-compatible bacterial ORFeomes and show its utility for comparative functional genomics.CONCLUSIONS:The E. coli ORFeome provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.

@article{Rajagopala2010Escherichia, abstract = {{BACKGROUND}:Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames ({ORFs}) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput {fashion.RESULTS}:We have constructed an open reading frame ({ORFeome}) collection of 3974 or 94\% of the known Escherichia coli K-12 {ORFs} in {Gateway(R}) entry vector {pENTR}/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among {YgjD}, {YjeE} and {YeaZ} proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this {ORFeome} with other Gateway-compatible bacterial {ORFeomes} and show its utility for comparative functional {genomics.CONCLUSIONS}:The E. coli {ORFeome} provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other {ORFeomes} makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Rajagopala, Seesandra and Yamamoto, Natsuko and Zweifel, Adrienne and Nakamichi, Tomoko and Huang, Hsi K. and Rios, Jorge M. and Koh, Jonathan F. and Boorgula, Meher and Fujita, Kazutoshi and Suzuki, Ken I. and Hu, James and Wanner, Barry and Mori, Hirotada and Uetz, Peter}, biburl = {https://www.bibsonomy.org/bibtex/2cecb088e68a7c437b2bccc3ffe33fec5/karthikraman}, citeulike-article-id = {7656586}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-11-470}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20701780}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20701780}, day = 11, doi = {10.1186/1471-2164-11-470}, interhash = {f77cccd8021688758194ff0b7299bde8}, intrahash = {cecb088e68a7c437b2bccc3ffe33fec5}, issn = {1471-2164}, journal = {BMC Genomics}, keywords = {comparative-analysis ecoli}, month = aug, number = 1, pages = {470+}, pmid = {20701780}, posted-at = {2010-08-16 09:27:29}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {The Escherichia coli K-12 {ORFeome}: a resource for comparative molecular microbiology}, url = {http://dx.doi.org/10.1186/1471-2164-11-470}, volume = 11, year = 2010 }