SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
<p>Abstract</p> <p>Background</p> <p>Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called <it>exonization</it>), or the element inserts into the exon, leading t...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-11-01
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| Series: | BMC Genetics |
| Online Access: | http://www.biomedcentral.com/1471-2156/8/78 |
| _version_ | 1818216690177015808 |
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| author | Suhai Sándor Ast Gil Sela Noa Mersch Britta Hotz-Wagenblatt Agnes |
| author_facet | Suhai Sándor Ast Gil Sela Noa Mersch Britta Hotz-Wagenblatt Agnes |
| author_sort | Suhai Sándor |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called <it>exonization</it>), or the element inserts into the exon, leading to a new transcript. Several examples in the literature show that isoforms generated by an exonization are specific to a certain tissue (for example the heart muscle) or inflict a disease. Thus, exonizations can have negative effects for the transcriptome of an organism.</p> <p>Results</p> <p>As we aimed at detecting other tissue- or tumor-specific isoforms in human and mouse genomes which were generated through exonization of a transposed element, we designed the automated analysis pipeline <it>SERpredict </it>(SER = Specific Exonized Retroelement) making use of Bayesian Statistics. With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.</p> <p>Conclusion</p> <p>Our results show that <it>SERpredict </it>produces relevant results, demonstrating the importance of transposed elements in shaping both the human and the mouse transcriptomes. The effect of transposed elements on the human transcriptome is several times higher than the effect on the mouse transcriptome, due to the contribution of the primate-specific Alu elements.</p> |
| first_indexed | 2024-12-12T06:55:59Z |
| format | Article |
| id | doaj.art-6f26b311b3374ff1b69b140dcccc05ac |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-12T06:55:59Z |
| publishDate | 2007-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-6f26b311b3374ff1b69b140dcccc05ac2022-12-22T00:33:58ZengBMCBMC Genetics1471-21562007-11-01817810.1186/1471-2156-8-78SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elementsSuhai SándorAst GilSela NoaMersch BrittaHotz-Wagenblatt Agnes<p>Abstract</p> <p>Background</p> <p>Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called <it>exonization</it>), or the element inserts into the exon, leading to a new transcript. Several examples in the literature show that isoforms generated by an exonization are specific to a certain tissue (for example the heart muscle) or inflict a disease. Thus, exonizations can have negative effects for the transcriptome of an organism.</p> <p>Results</p> <p>As we aimed at detecting other tissue- or tumor-specific isoforms in human and mouse genomes which were generated through exonization of a transposed element, we designed the automated analysis pipeline <it>SERpredict </it>(SER = Specific Exonized Retroelement) making use of Bayesian Statistics. With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.</p> <p>Conclusion</p> <p>Our results show that <it>SERpredict </it>produces relevant results, demonstrating the importance of transposed elements in shaping both the human and the mouse transcriptomes. The effect of transposed elements on the human transcriptome is several times higher than the effect on the mouse transcriptome, due to the contribution of the primate-specific Alu elements.</p>http://www.biomedcentral.com/1471-2156/8/78 |
| spellingShingle | Suhai Sándor Ast Gil Sela Noa Mersch Britta Hotz-Wagenblatt Agnes SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements BMC Genetics |
| title | SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements |
| title_full | SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements |
| title_fullStr | SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements |
| title_full_unstemmed | SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements |
| title_short | SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements |
| title_sort | serpredict detection of tissue or tumor specific isoforms generated through exonization of transposable elements |
| url | http://www.biomedcentral.com/1471-2156/8/78 |
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