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...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Suhai Sándor [verfasserIn] Ast Gil [verfasserIn] Sela Noa [verfasserIn] Mersch Britta [verfasserIn] Hotz-Wagenblatt Agnes [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2007

Übergeordnetes Werk:	In: BMC Genetics - BMC, 2003, 8(2007), 1, p 78
Übergeordnetes Werk:	volume:8 ; year:2007 ; number:1, p 78

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2156-8-78

Katalog-ID:	DOAJ042262674

Internformat


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author_variant	s s ss a g ag s n sn m b mb h w a hwa
matchkey_str	article:14712156:2007----::epeiteetootsuotmrpcfcsfrseeaetruhxnz
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publishDate	2007
allfields	10.1186/1471-2156-8-78 doi (DE-627)DOAJ042262674 (DE-599)DOAJ6f26b311b3374ff1b69b140dcccc05ac DE-627 ger DE-627 rakwb eng QH426-470 Suhai Sándor verfasserin aut SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 2007 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Genetics Ast Gil verfasserin aut Sela Noa verfasserin aut Mersch Britta verfasserin aut Hotz-Wagenblatt Agnes verfasserin aut In BMC Genetics BMC, 2003 8(2007), 1, p 78 (DE-627)326644938 (DE-600)2041497-3 14712156 nnns volume:8 year:2007 number:1, p 78 https://doi.org/10.1186/1471-2156-8-78 kostenfrei https://doaj.org/article/6f26b311b3374ff1b69b140dcccc05ac kostenfrei http://www.biomedcentral.com/1471-2156/8/78 kostenfrei https://doaj.org/toc/1471-2156 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2007 1, p 78
spelling	10.1186/1471-2156-8-78 doi (DE-627)DOAJ042262674 (DE-599)DOAJ6f26b311b3374ff1b69b140dcccc05ac DE-627 ger DE-627 rakwb eng QH426-470 Suhai Sándor verfasserin aut SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 2007 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Genetics Ast Gil verfasserin aut Sela Noa verfasserin aut Mersch Britta verfasserin aut Hotz-Wagenblatt Agnes verfasserin aut In BMC Genetics BMC, 2003 8(2007), 1, p 78 (DE-627)326644938 (DE-600)2041497-3 14712156 nnns volume:8 year:2007 number:1, p 78 https://doi.org/10.1186/1471-2156-8-78 kostenfrei https://doaj.org/article/6f26b311b3374ff1b69b140dcccc05ac kostenfrei http://www.biomedcentral.com/1471-2156/8/78 kostenfrei https://doaj.org/toc/1471-2156 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2007 1, p 78
allfields_unstemmed	10.1186/1471-2156-8-78 doi (DE-627)DOAJ042262674 (DE-599)DOAJ6f26b311b3374ff1b69b140dcccc05ac DE-627 ger DE-627 rakwb eng QH426-470 Suhai Sándor verfasserin aut SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 2007 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Genetics Ast Gil verfasserin aut Sela Noa verfasserin aut Mersch Britta verfasserin aut Hotz-Wagenblatt Agnes verfasserin aut In BMC Genetics BMC, 2003 8(2007), 1, p 78 (DE-627)326644938 (DE-600)2041497-3 14712156 nnns volume:8 year:2007 number:1, p 78 https://doi.org/10.1186/1471-2156-8-78 kostenfrei https://doaj.org/article/6f26b311b3374ff1b69b140dcccc05ac kostenfrei http://www.biomedcentral.com/1471-2156/8/78 kostenfrei https://doaj.org/toc/1471-2156 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2007 1, p 78
allfieldsGer	10.1186/1471-2156-8-78 doi (DE-627)DOAJ042262674 (DE-599)DOAJ6f26b311b3374ff1b69b140dcccc05ac DE-627 ger DE-627 rakwb eng QH426-470 Suhai Sándor verfasserin aut SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 2007 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Genetics Ast Gil verfasserin aut Sela Noa verfasserin aut Mersch Britta verfasserin aut Hotz-Wagenblatt Agnes verfasserin aut In BMC Genetics BMC, 2003 8(2007), 1, p 78 (DE-627)326644938 (DE-600)2041497-3 14712156 nnns volume:8 year:2007 number:1, p 78 https://doi.org/10.1186/1471-2156-8-78 kostenfrei https://doaj.org/article/6f26b311b3374ff1b69b140dcccc05ac kostenfrei http://www.biomedcentral.com/1471-2156/8/78 kostenfrei https://doaj.org/toc/1471-2156 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2007 1, p 78
allfieldsSound	10.1186/1471-2156-8-78 doi (DE-627)DOAJ042262674 (DE-599)DOAJ6f26b311b3374ff1b69b140dcccc05ac DE-627 ger DE-627 rakwb eng QH426-470 Suhai Sándor verfasserin aut SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 2007 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Genetics Ast Gil verfasserin aut Sela Noa verfasserin aut Mersch Britta verfasserin aut Hotz-Wagenblatt Agnes verfasserin aut In BMC Genetics BMC, 2003 8(2007), 1, p 78 (DE-627)326644938 (DE-600)2041497-3 14712156 nnns volume:8 year:2007 number:1, p 78 https://doi.org/10.1186/1471-2156-8-78 kostenfrei https://doaj.org/article/6f26b311b3374ff1b69b140dcccc05ac kostenfrei http://www.biomedcentral.com/1471-2156/8/78 kostenfrei https://doaj.org/toc/1471-2156 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2007 1, p 78
language	English
source	In BMC Genetics 8(2007), 1, p 78 volume:8 year:2007 number:1, p 78
sourceStr	In BMC Genetics 8(2007), 1, p 78 volume:8 year:2007 number:1, p 78
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Genetics
isfreeaccess_bool	true
container_title	BMC Genetics
authorswithroles_txt_mv	Suhai Sándor @@aut@@ Ast Gil @@aut@@ Sela Noa @@aut@@ Mersch Britta @@aut@@ Hotz-Wagenblatt Agnes @@aut@@
publishDateDaySort_date	2007-01-01T00:00:00Z
hierarchy_top_id	326644938
id	DOAJ042262674
language_de	englisch
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callnumber-first	Q - Science
author	Suhai Sándor
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topic_title	QH426-470 SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
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title	SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
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title_full	SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
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title_sort	serpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
callnumber	QH426-470
title_auth	SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
abstract	<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<
abstractGer	<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<
abstract_unstemmed	<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<
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