Enrichment of transcriptional regulatory sites in non-coding genomic region
Identifieur interne : 000110 ( Istex/Corpus ); précédent : 000109; suivant : 000111Enrichment of transcriptional regulatory sites in non-coding genomic region
Auteurs : Wen Xue ; Jin Wang ; Zhirong Shen ; Huaiqiu ZhuSource :
- Bioinformatics [ 1367-4803 ] ; 2004.
English descriptors
- Teeft :
- Actual occurrence, Algorithm, Bioinformatics, Codon, Computational, Consensus sequence, Consensus sequences, Different classes, Different sources, Drosophila, Drosophila genome, Enrichment, Enrichment analysis, Exon, Exon region, Genome, Genome sequence, Genomic, Genomic region, Genomic regions, Intergenic, Intergenic region, Intergenic regions, Intron, Intron region, Intron regions, Natl acad, Promoter, Random sequences, Regulatory signals, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Scpd, Sexon, Simple method, Sintron, Systematic analysis, Transcriptional, Whole genome, Yeast.
Abstract
Motivation: Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment. Results: To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions. Availability: Free programs are available at http://dii.nju.edu.cn/~xuewen/enrichment/
Url:
DOI: 10.1093/bioinformatics/btg450
Links to Exploration step
ISTEX:EE32BA100EE4974F7F4E6B7DE46086C5A549732ALe document en format XML
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Huaiqiu" sort="Zhu, Huaiqiu" uniqKey="Zhu H" first="Huaiqiu" last="Zhu">Huaiqiu Zhu</name><affiliation><mods:affiliation>The Center for Theoretical Biology, Beijing University, Beijing 100781, China</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="e-published">2004</date><date type="published">2004</date><biblScope unit="vol">20</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="569">569</biblScope><biblScope unit="page" to="575">575</biblScope></imprint><idno type="ISSN">1367-4803</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Actual 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genome</term><term>Yeast</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment. Results: To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions. 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This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment. Results: To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions. Availability: Free programs are available at http://dii.nju.edu.cn/~xuewen/enrichment/</abstract><qualityIndicators><score>7.862</score><pdfWordCount>4195</pdfWordCount><pdfCharCount>27031</pdfCharCount><pdfVersion>1.4</pdfVersion><pdfPageCount>7</pdfPageCount><pdfPageSize>595 x 841 pts</pdfPageSize><pdfWordsPerPage>599</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>false</refBibsNative><abstractWordCount>316</abstractWordCount><abstractCharCount>2156</abstractCharCount><keywordCount>0</keywordCount></qualityIndicators><title>Enrichment of transcriptional regulatory sites in non-coding genomic region</title><pmid><json:string>14990453</json:string></pmid><genre><json:string>other</json:string></genre><host><title>Bioinformatics</title><language><json:string>unknown</json:string></language><issn><json:string>1367-4803</json:string></issn><eissn><json:string>1460-2059</json:string></eissn><publisherId><json:string>bioinformatics</json:string></publisherId><volume>20</volume><issue>4</issue><pages><first>569</first><last>575</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>2004-01-22</json:string></date><geogName></geogName><orgName><json:string>The Center for Theoretical Biology</json:string><json:string>Beijing University</json:string><json:string>Oxford University</json:string><json:string>China Received</json:string><json:string>National Science Foundation of China</json:string></orgName><orgName_funder><json:string>National Science Foundation of China</json:string></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Snc</json:string><json:string>Sintron</json:string><json:string>Peter Markstein</json:string></persName><placeName><json:string>Beijing</json:string><json:string>Berkeley</json:string></placeName><ref_url><json:string>http://dii.nju.edu</json:string></ref_url><ref_bibl><json:string>Zhu and Zhang, 1999</json:string><json:string>Wang et al., 1999</json:string><json:string>Lee et al., 2002</json:string><json:string>Simon et al., 2001</json:string><json:string>Adams et al., 2000</json:string><json:string>Markstein et al., 2002</json:string><json:string>Matys et al., 2003</json:string><json:string>Hertz and Stormo, 1999</json:string><json:string>Zhang, 2002</json:string><json:string>Levy et al. (2001)</json:string><json:string>Baer et al., 1984</json:string><json:string>W.Xue et al.</json:string><json:string>Van Helden et al., 1998</json:string><json:string>Ptashne and Gann, 1997</json:string><json:string>Hutchinson, 1996</json:string><json:string>Carey et al., 1992</json:string><json:string>Brazma et al., 1998</json:string><json:string>Lieb et al., 2001</json:string><json:string>Lehman et al., 1998</json:string><json:string>Xie et al., 1999</json:string><json:string>Iyer et al., 2001</json:string><json:string>Sinha and Tompa, 2002</json:string><json:string>Wood et al., 2002</json:string><json:string>Pilpel et al., 2001</json:string><json:string>Kel-Margoulis et al., 2003</json:string><json:string>Berman et al., 2002</json:string><json:string>Goffeau et al., 1996</json:string><json:string>Hampson et al., 2002</json:string><json:string>Hughes et al., 2000</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/HXZ-VBQJG27J-M</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - mathematical & computational biology</json:string><json:string>2 - biotechnology & applied microbiology</json:string><json:string>2 - biochemical research methods</json:string></wos><scienceMetrix><json:string>1 - applied sciences</json:string><json:string>2 - enabling & strategic technologies</json:string><json:string>3 - bioinformatics</json:string></scienceMetrix><scopus><json:string>1 - Physical Sciences</json:string><json:string>2 - Mathematics</json:string><json:string>3 - Computational Mathematics</json:string><json:string>1 - Physical Sciences</json:string><json:string>2 - Computer Science</json:string><json:string>3 - Computational Theory and Mathematics</json:string><json:string>1 - Physical Sciences</json:string><json:string>2 - Computer Science</json:string><json:string>3 - Computer Science Applications</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Molecular Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Biochemistry</json:string><json:string>1 - Physical Sciences</json:string><json:string>2 - Mathematics</json:string><json:string>3 - Statistics and Probability</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>2004</publicationDate><copyrightDate>2004</copyrightDate><doi><json:string>10.1093/bioinformatics/btg450</json:string></doi><id>EE32BA100EE4974F7F4E6B7DE46086C5A549732A</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/HXZ-VBQJG27J-M/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/HXZ-VBQJG27J-M/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/HXZ-VBQJG27J-M/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main">Enrichment of transcriptional regulatory sites in non-coding genomic region</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Oxford University Press</publisher><availability><licence><hi rend="italic">Bioinformatics</hi> 20(4) © Oxford University Press 2004; all rights reserved.</licence></availability><date type="published">2004</date><date type="Copyright" when="2004">2004</date></publicationStmt><notesStmt><note type="content-type" source="other" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</note><note type="publication-type" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="other"><analytic><title level="a" type="main">Enrichment of transcriptional regulatory sites in non-coding genomic region</title><author xml:id="author-0000"><persName><surname>Xue</surname><forename type="first">Wen</forename></persName><affiliation role="corresp">Contact: jwang@nju.edu.cn</affiliation></author><author xml:id="author-0001"><persName><surname>Wang</surname><forename type="first">Jin</forename></persName><affiliation role="corresp">Contact: jwang@nju.edu.cn</affiliation></author><author xml:id="author-0002"><persName><surname>Shen</surname><forename type="first">Zhirong</forename></persName><affiliation role="corresp">Contact: jwang@nju.edu.cn</affiliation></author><author xml:id="author-0003"><persName><surname>Zhu</surname><forename type="first">Huaiqiu</forename></persName><affiliation role="corresp">Contact: jwang@nju.edu.cn</affiliation></author><idno type="istex">EE32BA100EE4974F7F4E6B7DE46086C5A549732A</idno><idno type="ark">ark:/67375/HXZ-VBQJG27J-M</idno><idno type="other">btg450</idno><idno type="DOI">10.1093/bioinformatics/btg450</idno></analytic><monogr><title level="j" type="main">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="hwp">bioinfo</idno><idno type="nlm-ta">Bioinformatics</idno><idno type="publisher-id">bioinformatics</idno><idno type="pISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="e-published">2004</date><date type="published">2004</date><biblScope unit="vol">20</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="569">569</biblScope><biblScope unit="page" to="575">575</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.41" when="2020-04-06"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract xml:lang="en"><p><hi rend="bold">Motivation:</hi> Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS <hi rend="italic">in silico</hi>. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the <hi rend="italic">Drosophila</hi> genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment.</p><p><hi rend="bold">Results:</hi> To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the <hi rend="italic">Saccharomyces cerevisiae</hi>, <hi rend="italic">Schizosaccharomyces pombe</hi> and Epstein-Barr virus (EBV) genomes. The enrichment of <hi rend="italic">S.cerevisiae</hi> TRS in the 600 bp upstream region of genes was also significant. In <hi rend="italic">Drosophila</hi> genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some <hi rend="italic">S.cerevisiae</hi> TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions.</p><p><hi rend="bold">Availability:</hi> Free programs are available at <ref type="url">http://dii.nju.edu.cn/~xuewen/enrichment/</ref></p></abstract><textClass ana="subject"><keywords scheme="heading"><term>Original Papers</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2020-04-06" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/HXZ-VBQJG27J-M/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup, element #text not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="US-ASCII"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article xml:lang="en" article-type="other"><front><journal-meta><journal-id journal-id-type="hwp">bioinfo</journal-id><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
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<contrib contrib-type="author"><name><surname>Xue</surname><given-names>Wen</given-names></name>
<xref rid="AFF1">1</xref>
</contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jin</given-names></name>
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<xref rid="FN1">*</xref>
</contrib><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Zhirong</given-names></name>
<xref rid="AFF1">1</xref>
</contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Huaiqiu</given-names></name>
<xref rid="AFF2">2</xref>
</contrib><aff><target target-type="aff" id="AFF1"></target><label>1</label>The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China and <target target-type="aff" id="AFF2"></target><label>2</label>The Center for Theoretical Biology, Beijing University, Beijing 100781, China</aff></contrib-group><author-notes><corresp><bold>Contact:</bold> <ext-link xlink:href="jwang@nju.edu.cn" ext-link-type="email">jwang@nju.edu.cn</ext-link></corresp></author-notes><pub-date pub-type="epub"><day>22</day><month>1</month><year>2004</year></pub-date><pub-date pub-type="ppub"><day>1</day><month>3</month><year>2004</year></pub-date><volume>20</volume><issue>4</issue><fpage>569</fpage><lpage>575</lpage><history><date date-type="accepted"><day>26</day><month>9</month><year>2003</year></date><date date-type="received"><day>22</day><month>7</month><year>2003</year></date><date date-type="rev-recd"><day>3</day><month>9</month><year>2003</year></date></history><permissions><copyright-statement><italic>Bioinformatics</italic> 20(4) © Oxford University Press 2004; all rights reserved.</copyright-statement><copyright-year>2004</copyright-year></permissions><abstract xml:lang="en">
<p><bold>Motivation:</bold> Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS <italic>in silico</italic>. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the <italic>Drosophila</italic> genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment.</p>
<p><bold>Results:</bold> To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the <italic>Saccharomyces cerevisiae</italic>, <italic>Schizosaccharomyces pombe</italic> and Epstein-Barr virus (EBV) genomes. The enrichment of <italic>S.cerevisiae</italic> TRS in the 600 bp upstream region of genes was also significant. In <italic>Drosophila</italic> genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some <italic>S.cerevisiae</italic> TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions.</p>
<p><bold>Availability:</bold> Free programs are available at <ext-link xlink:href="http://dii.nju.edu.cn/~xuewen/enrichment/" ext-link-type="url">http://dii.nju.edu.cn/~xuewen/enrichment/</ext-link></p>
</abstract><custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name><meta-value>569</meta-value></custom-meta><custom-meta><meta-name>hwp-legacy-dochead</meta-name><meta-value>Original Paper</meta-value></custom-meta></custom-meta-wrap></article-meta></front>
</article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Enrichment of transcriptional regulatory sites in non-coding genomic region</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>Enrichment of transcriptional regulatory sites in non-coding genomic region</title></titleInfo><name type="personal"><namePart type="given">Wen</namePart><namePart type="family">Xue</namePart><affiliation>The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China and</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jin</namePart><namePart type="family">Wang</namePart><affiliation>The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China and</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Zhirong</namePart><namePart type="family">Shen</namePart><affiliation>The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China and</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Huaiqiu</namePart><namePart type="family">Zhu</namePart><affiliation>The Center for Theoretical Biology, Beijing University, Beijing 100781, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="other" displayLabel="other" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-7474895G-0">other</genre><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2004-03-01</dateIssued><dateCreated encoding="w3cdtf">2003-09-26</dateCreated><copyrightDate encoding="w3cdtf">2004</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Motivation: Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment. Results: To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions. Availability: Free programs are available at http://dii.nju.edu.cn/~xuewen/enrichment/</abstract><note type="author-notes">Contact: jwang@nju.edu.cn</note><relatedItem type="host"><titleInfo><title>Bioinformatics</title></titleInfo><titleInfo type="abbreviated"><title>Bioinformatics</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><identifier type="ISSN">1367-4803</identifier><identifier type="eISSN">1460-2059</identifier><identifier type="PublisherID">bioinformatics</identifier><identifier type="PublisherID-hwp">bioinfo</identifier><identifier type="PublisherID-nlm-ta">Bioinformatics</identifier><part><date>2004</date><detail type="volume"><caption>vol.</caption><number>20</number></detail><detail type="issue"><caption>no.</caption><number>4</number></detail><extent unit="pages"><start>569</start><end>575</end></extent></part></relatedItem><identifier type="istex">EE32BA100EE4974F7F4E6B7DE46086C5A549732A</identifier><identifier type="ark">ark:/67375/HXZ-VBQJG27J-M</identifier><identifier type="DOI">10.1093/bioinformatics/btg450</identifier><identifier type="local">btg450</identifier><accessCondition type="use and reproduction" contentType="copyright">Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-GTWS0RDP-M">oup</recordContentSource><recordOrigin>Converted from (version 1.2.10) to MODS version 3.6.</recordOrigin><recordCreationDate encoding="w3cdtf">2020-04-17</recordCreationDate></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/HXZ-VBQJG27J-M/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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