Detecting novel genes with sparse arrays

Gene

Volumn 467, Issue 1-2, 2010, Pages 41-51

  Arvas, Mikko ^a   Haiminen, Niina ^b   Smit, Bart ^c   Rautio, Jari ^d   Vitikainen, Marika ^a   Wiebe, Marilyn ^a   Martinez, Diego ^e   Chee, Christine ^e   Kunkel, Joe ^e   Sanchez, Charles ^e   Nelson, Mary Anne ^e   Pakula, Tiina ^a   Saloheimo, Markku ^a   Penttilä, Merja ^a   Kivioja, Teemu ^b  

^a VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c FRIESLANDCAMPINA   (Netherlands)

^d Plexpress   (Finland)

^e UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Gene prediction; Microarray; Moulds; Transcript

Indexed keywords

ARTICLE; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME; GENOME ANALYSIS; HYPOCREA JECORINA; MICROARRAY ANALYSIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; BIOLOGY; DNA MICROARRAY; FUNGAL GENE; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENETICS; PROCEDURES; SPECIES DIFFERENCE; TRICHODERMA;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES, FUNGAL; GENOME, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; SPECIES SPECIFICITY; TRICHODERMA;

FUNGI; HYPOCREA JECORINA;

MESSENGER RNA;

EID: 77956902625     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2010.07.009     Document Type: Article

References (59)

1. Altschul S., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Amaral P.P., Dinger M.E., R., M.T., Mattick J.S. The eukaryotic genome as an RNA machine. Science 2008, 319:1787-1789.
4. Arvas M., et al. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics 2007, 8.
5. Arvas M., et al. Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics 2006, 7:32.
6. Bertone P., et al. Global identification of human transcribed sequences with genome tiling arrays. Science 2004, 306:2242-2246.
7. Brent M. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat. Rev. Genet. 2008, 9:62-74.
8. Cai J., Woo P., Lau S., D.K., S., K., Y. Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J. Mol. Evol. 2006, 63:1-11.
9. Chambergo F., et al. Elucidation of the metabolic fate of glucose in the filamentous fungus Trichoderma reesei using expressed sequence tag (EST) analysis and cDNA microarrays. J. Biol. Chem. 2002, 277:13983-13988.
10. Cherry J., Fidantsef A. Directed evolution of industrial enzymes: an update. Curr. Opin. Biotechnol. 2003, 14:438-443.
11. Chou C., Chen C., Lee T., Peck K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 2004, 32:e99.
12. David L., et al. A high-resolution map of transcription in the yeast genome. Proc. Nat. Acad. Sci. 2006, 103:5320-5325.
13. Dinger M., Pang K., Mercer T., Mattick J. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput. Biol. 2008, 4.
14. Edgar R., Domrachev M., Lash A. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207.
15. Fedorova N.D., et al. Genomic islands in the pathogenic filamentous fungus aspergillus fumigatus. PLoS Genet. 2008, 4:e1000046.
16. Foreman P., et al. Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei. J. Biol. Chem. 2003, 278:31988-31997.
17. Gentleman R.C., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
18. Gingeras T.R. Origin of phenotypes: genes and transcripts. Genome Res. 2007, 17:682-690. http://www.genome.org/cgi/reprint/17/6/682.pdf.
19. Griffiths-Jones S., Bateman A., Marshall M., Khanna A., Eddy S. Rfam: an RNA family database. Nucleic Acids Res. 2003, 31:439.
20. Hughes T., et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 2001, 19:342-347.
21. Irizarry R., Bolstad B., Collin F., Cope L., Hobbs B., Speed T. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31:e15.
22. Jensen L., Ussery D., Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Res. 2003, 13:2444.
23. Juneau K., Palm C., Miranda M., Davis R. High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc. Nat. Acad. Sci. 2007, 104:1522.
24. Kamper J., et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006, 444:97-101.
25. Kawahara Y., Imanishi T. A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evol. Biol. 2007, 7:13.
26. Khaldi N., Collemare J., Lebrun M., Wolfe K. Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol. 2008, 9:R18.
27. Lieckfeldt E., Kullnig C., Samuels G., Kubicek C. Sexually competent, sucrose-and nitrate-assimilating strains of Hypocrea jecorina (Trichoderma reesei) from South American soils. Mycologia 2000, 92:374-380.
28. Machida M., et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 2005, 438:1157-1161.
29. Marshall O. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 2004, 20:2471.
30. Martinez D., et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat. Biotechnol. 2008, 26:553-560.
31. Mignone F., et al. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2005, 33:D141.
32. Miura F., et al. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc. Nat. Acad. Sci. 2006, 103:17846.
33. Montenecourt B.S., Eveleigh D.E. Selective screening methods for the isolation of high yielding cellulase mutants of Trichoderma reesei. Adv. Chem. Ser. 1979, 181:289-301.
34. Mulder N., et al. InterPro, progress and status in 2005. Nucleic Acids Res. 2005, 33:D201.
35. Nagalakshmi U., et al. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science 2008, 320:1344-1349.
36. Naumov G., Naumova E., Sancho E., Korhbla M. Polymeric SUC genes in natural populations of Saccharomyces cerevisiae. FEMS Microbiol. Lett. 1996, 135:31-35.
37. Pakula T., Salonen K., Uusitalo J., Penttilä M. The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei. Microbiology 2005, 151:135-143.
38. van de Peppel J., Kemmeren P., van Bakel H., Radonjic M., van Leenen D., Holstege F. Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep. 2003, 4:387.
39. Ponjavic J., Ponting C., Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 2007, 17:556.
40. Quevillon E., et al. Interproscan: protein domains identifier. Nucleic Acids Res. 2005, 33:W116-20.
41. Development Core Team R. R: A Language and Environment for Statistical Computing 2008, R Foundation for Statistical Computing, Vienna, Austria.
42. Rautio J., Smit B., Wiebe M., Penttilä M., Saloheimo M. Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei. BMC Genomics 2006, 7:247.
43. Rehmeyer C., et al. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Res. 2006, 34:4685-4701.
44. Rice P., Longden I., Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000, 16:276-277.
45. Rodriguez A., Griffiths-Jones S., Ashurst J., Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004, 14:1902.
46. Royce T., et al. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 2005, 21:466-475.
47. Royce T., Rozowsky J., Gerstein M. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 2007, 23:988.
48. Ruepp A., et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32:5539.
49. Samanta M., Tongprasit W., Sethi H., Chin C.S., Stolc V. Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc. Nat. Acad. Sci. 2006, 103:4192-4197.
50. Selinger D., et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 2000, 18:1262-1268.
51. Stajich J., et al. The Bioperl toolkit: Perl Modules for the life sciences. Genome Res. 2002, 12:1611.
52. Stanke M., Diekhans M., Baertsch R., Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 2008, 24:637.
53. Stein L., et al. The generic genome browser: a building block for a model organism system database. Genome Res. 2002, 12:1599-1610.
54. Strauss J., et al. Crel, the carbon catabolite repressor protein from Trichoderma reesei. FEBS Lett. 1995, 376:103-107.
55. Ter-Hovhannisyan V., Lomsadze A., Chernoff Y., Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008, 18:1979.
56. Valkonen M., Penttilä M., Saloheimo M. The ire1 and ptc2 genes involved in the unfolded protein response pathway in the filamentous fungus Trichoderma reesei. Mol. Genet. Genomics 2004, 272:443-451.
57. Warren A., Archuleta J., Feng W., Setubal J. Missing genes in the annotation of prokaryotic genomes. BMC Bioinform. 2010, 11:131.
58. Wilhelm B., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243.
59. Zhao Y., et al. MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Genet. 2008, 24:323-327.