Detecting novel genes with sparse arrays

Mikko Arvas (Corresponding Author), Niina Haiminen, Bart Smit, Jari Rautio, Marika Vitikainen, Marilyn Wiebe, Diego Martinez, Christine Chee, Joe Kunkel, Charles Sanchez, Mary Anne Nelson, Tiina Pakula, Markku Saloheimo, Merja Penttilä, Teemu Kivioja

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

Abstract

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions.We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9. Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100. b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties.

Original languageEnglish
Pages (from-to)41-51
JournalGene
Volume467
Issue number1-2
DOIs
Publication statusPublished - 1 Nov 2010
MoE publication typeA1 Journal article-refereed

Fingerprint

Genes
Genome
Costs and Cost Analysis
Trichoderma
Intergenic DNA
Oligonucleotide Probes
Regulator Genes
Microarray Analysis
Fungi
Phenotype
Proteins

Keywords

  • Gene prediction
  • Microarray
  • Moulds
  • Transcript

Cite this

Arvas, M., Haiminen, N., Smit, B., Rautio, J., Vitikainen, M., Wiebe, M., ... Kivioja, T. (2010). Detecting novel genes with sparse arrays. Gene, 467(1-2), 41-51. https://doi.org/10.1016/j.gene.2010.07.009
Arvas, Mikko ; Haiminen, Niina ; Smit, Bart ; Rautio, Jari ; Vitikainen, Marika ; Wiebe, Marilyn ; Martinez, Diego ; Chee, Christine ; Kunkel, Joe ; Sanchez, Charles ; Nelson, Mary Anne ; Pakula, Tiina ; Saloheimo, Markku ; Penttilä, Merja ; Kivioja, Teemu. / Detecting novel genes with sparse arrays. In: Gene. 2010 ; Vol. 467, No. 1-2. pp. 41-51.
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Arvas, M, Haiminen, N, Smit, B, Rautio, J, Vitikainen, M, Wiebe, M, Martinez, D, Chee, C, Kunkel, J, Sanchez, C, Nelson, MA, Pakula, T, Saloheimo, M, Penttilä, M & Kivioja, T 2010, 'Detecting novel genes with sparse arrays', Gene, vol. 467, no. 1-2, pp. 41-51. https://doi.org/10.1016/j.gene.2010.07.009

Detecting novel genes with sparse arrays. / Arvas, Mikko (Corresponding Author); Haiminen, Niina; Smit, Bart; Rautio, Jari; Vitikainen, Marika; Wiebe, Marilyn; Martinez, Diego; Chee, Christine; Kunkel, Joe; Sanchez, Charles; Nelson, Mary Anne; Pakula, Tiina; Saloheimo, Markku; Penttilä, Merja; Kivioja, Teemu.

In: Gene, Vol. 467, No. 1-2, 01.11.2010, p. 41-51.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Arvas, Mikko

AU - Haiminen, Niina

AU - Smit, Bart

AU - Rautio, Jari

AU - Vitikainen, Marika

AU - Wiebe, Marilyn

AU - Martinez, Diego

AU - Chee, Christine

AU - Kunkel, Joe

AU - Sanchez, Charles

AU - Nelson, Mary Anne

AU - Pakula, Tiina

AU - Saloheimo, Markku

AU - Penttilä, Merja

AU - Kivioja, Teemu

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Arvas M, Haiminen N, Smit B, Rautio J, Vitikainen M, Wiebe M et al. Detecting novel genes with sparse arrays. Gene. 2010 Nov 1;467(1-2):41-51. https://doi.org/10.1016/j.gene.2010.07.009