Computational identification of operon-like transcriptional loci in eukaryotes

Computers in Biology and Medicine

Volumn 43, Issue 6, 2013, Pages 738-743

  Nannapaneni, Kishore ^a   Ben Shahar, Yehuda ^a,c,d   Keen, Henry L ^a,c   Welsh, Michael J ^a,c   Casavant, Thomas L ^a,b   Scheetz, Todd E ^a,b  

^a UNIVERSITY OF IOWA   (United States)

^b University of Iowa   (United States)

^c UNIVERSITY OF IOWA   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Computational; Drosophila; Eukaryote; Operon; Poly cistronic; Trans spliced

Indexed keywords

COMPUTATIONAL; DROSOPHILA; EUKARYOTE; OPERON; POLY-CISTRONIC; TRANS-SPLICED;

BIOLOGY; COMPUTER APPLICATIONS;

GENE EXPRESSION;

MESSENGER RNA PRECURSOR;

ARTICLE; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE EXPRESSION; OPERON; PRIORITY JOURNAL; RNA SPLICING;

ANIMALS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENETIC LOCI; OPERON; RNA SPLICING; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84877701691     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2013.03.004     Document Type: Article

References (15)

1. T. Blumenthal Trans-splicing and Operons, in: The C.elegans Research Community (Ed.), WormBook, 1(1). http://doi/10.1895/wormbook%202005.
2. Spieth J., Brooke G., Kuersten S., Lea K., Blumenthal T. Operons in C. elegans: polycistronic mRNA precursors are processed by trans-splicing of SL2 to downstream coding regions. Cell 1993, 73(3):521-532.
3. Blumenthal T., Evans D., Link C.D., Guffanti A., Lawson D., Thierry-Mieg J., Thierry-Mieg D., Chiu W.L., Duke K., Kiraly M. A global analysis of Caenorhabditis elegans operons. Nature 2002, 417:851-854.
4. Blumenthal T. Operons in eukaryotes. Brief. Funct. Genomic. Proteomic. 2004, 3(3):199-211.
5. Ben-Shahar Y., Nannapaneni K., Casavant T.L., Scheetz T.E., Welsh M.J. Eukaryotic operon-like transcription of functionally related genes in Drosophila. Proc. Natl. Acad. Sci. U. S. A. 2007, 104(1):222-227.
6. Lin H., Mann K.J., Starostina E, Kinser R.D., Pikielny C.W. A. Drosophila DEG/ENaC channel subunit is required for male response to female pheromones. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(36):12831-12836.
7. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster Analysis and Display of Genome-Wide Expression Patterns, PNAS. 1998, 95(25):14863-14868.
8. Reese M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 2001, 26(1):51-56.
9. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25(1):25-29.
10. Hubbard T.J., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., Down T., Dyer S.C., Fitzgerald S., Fernandez-Banet J., Graf S, Haider S., Hammond M., Herrero J., Holland R., Howe K., Howe K., Johnson N., Kahari A., Keefe D., Kokocinski F., Kulesha E., Lawson D., Longden I., Melsopp C., Megy K., Meidl P., Ouverdin B., Parker A., Prlic A., Rice S., Rios D., Schuster M., Sealy I., Severin J., Slater G., Smedley D., Spudich G., Trevanion S., Vilella A., Vogel J., White S., Wood M., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Flicek P., Kasprzyk A., Proctor G., Searle S., Smith J., Ureta-Vidal A., Birney E. Ensembl 2007. Nucleic Acids Res. 2007, 35:D610-7. Database issue.
11. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Rudnev D., Evangelista C., Kim I.F., Soboleva A., Tomashevsky M., Edgar R., NCBI GEO mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res. 2007, 35:D760-5. Database issue.
12. Boguski M.S., Lowe T.M.J., Tolstoshev C.M. dbEST - database forexpressed sequence tags. Nat. Genet. 1993, 4(4):332-333.
13. Bailey T.L., Williams N., Misleh C., Li W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34:W369-W373. Web Server issue.
14. Land M., Islas-Trejo A., Rubin C.S. Origin, properties, and regulated expression of multiple mRNAs encoded by the protein kinase C1 gene of Caenorhabditis elegans. J. Biol. Chem. 1994, 269(20):14820-14827.
15. Quijano C., Tomancak P., Lopez-Marti J., Suyama M., Bork P., Milan M., Torrents D., Manzanares M. Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Genome Biol. 2008, 9(12):R176.