Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
Identifieur interne : 002341 ( Istex/Corpus ); précédent : 002340; suivant : 002342Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
Auteurs : Yee Leng Yap ; Maria P. Wong ; Xue Wu Zhang ; David Hernandez ; Robin Gras ; David K. Smith ; Antoine DanchinSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2005.
Abstract
Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.
Url:
DOI: 10.1093/nar/gki188
Links to Exploration step
ISTEX:0BFC1DB5DBE0149707002F146869EB08D51A995CLe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
<author><name sortKey="Yap, Yee Leng" sort="Yap, Yee Leng" uniqKey="Yap Y" first="Yee Leng" last="Yap">Yee Leng Yap</name>
<affiliation><mods:affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Wong, Maria P" sort="Wong, Maria P" uniqKey="Wong M" first="Maria P." last="Wong">Maria P. Wong</name>
<affiliation><mods:affiliation>Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name>
<affiliation><mods:affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Hernandez, David" sort="Hernandez, David" uniqKey="Hernandez D" first="David" last="Hernandez">David Hernandez</name>
<affiliation><mods:affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Gras, Robin" sort="Gras, Robin" uniqKey="Gras R" first="Robin" last="Gras">Robin Gras</name>
<affiliation><mods:affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Smith, David K" sort="Smith, David K" uniqKey="Smith D" first="David K." last="Smith">David K. Smith</name>
<affiliation><mods:affiliation>Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Danchin, Antoine" sort="Danchin, Antoine" uniqKey="Danchin A" first="Antoine" last="Danchin">Antoine Danchin</name>
<affiliation><mods:affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</mods:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:0BFC1DB5DBE0149707002F146869EB08D51A995C</idno>
<date when="2005" year="2005">2005</date>
<idno type="doi">10.1093/nar/gki188</idno>
<idno type="url">https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/fulltext/pdf</idno>
<idno type="wicri:Area/Istex/Corpus">002341</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002341</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
<author><name sortKey="Yap, Yee Leng" sort="Yap, Yee Leng" uniqKey="Yap Y" first="Yee Leng" last="Yap">Yee Leng Yap</name>
<affiliation><mods:affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</mods:affiliation>
</affiliation>
<affiliation><mods:affiliation>To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Wong, Maria P" sort="Wong, Maria P" uniqKey="Wong M" first="Maria P." last="Wong">Maria P. Wong</name>
<affiliation><mods:affiliation>Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name>
<affiliation><mods:affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Hernandez, David" sort="Hernandez, David" uniqKey="Hernandez D" first="David" last="Hernandez">David Hernandez</name>
<affiliation><mods:affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Gras, Robin" sort="Gras, Robin" uniqKey="Gras R" first="Robin" last="Gras">Robin Gras</name>
<affiliation><mods:affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Smith, David K" sort="Smith, David K" uniqKey="Smith D" first="David K." last="Smith">David K. Smith</name>
<affiliation><mods:affiliation>Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China</mods:affiliation>
</affiliation>
</author>
<author><name sortKey="Danchin, Antoine" sort="Danchin, Antoine" uniqKey="Danchin A" first="Antoine" last="Danchin">Antoine Danchin</name>
<affiliation><mods:affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</mods:affiliation>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Nucleic Acids Research</title>
<title level="j" type="abbrev">Nucl. Acids Res.</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><publisher>Oxford University Press</publisher>
<date type="published" when="2005">2005</date>
<biblScope unit="volume">33</biblScope>
<biblScope unit="issue">1</biblScope>
<biblScope unit="page" from="409">409</biblScope>
<biblScope unit="page" to="421">421</biblScope>
</imprint>
<idno type="ISSN">0305-1048</idno>
</series>
<idno type="istex">0BFC1DB5DBE0149707002F146869EB08D51A995C</idno>
<idno type="DOI">10.1093/nar/gki188</idno>
<idno type="local">gki188</idno>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">0305-1048</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass></textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.</div>
</front>
</TEI>
<istex><corpusName>oup</corpusName>
<author><json:item><name>Yee Leng Yap</name>
<affiliations><json:string>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</json:string>
<json:string>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</json:string>
<json:string>To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</json:string>
</affiliations>
</json:item>
<json:item><name>Maria P. Wong</name>
<affiliations><json:string>Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China</json:string>
</affiliations>
</json:item>
<json:item><name>Xue Wu Zhang</name>
<affiliations><json:string>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</json:string>
</affiliations>
</json:item>
<json:item><name>David Hernandez</name>
<affiliations><json:string>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</json:string>
</affiliations>
</json:item>
<json:item><name>Robin Gras</name>
<affiliations><json:string>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</json:string>
</affiliations>
</json:item>
<json:item><name>David K. Smith</name>
<affiliations><json:string>Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China</json:string>
</affiliations>
</json:item>
<json:item><name>Antoine Danchin</name>
<affiliations><json:string>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</json:string>
</affiliations>
</json:item>
</author>
<subject><json:item><lang><json:string>eng</json:string>
</lang>
<value>24</value>
</json:item>
</subject>
<language><json:string>eng</json:string>
</language>
<originalGenre><json:string>other</json:string>
</originalGenre>
<abstract>Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.</abstract>
<qualityIndicators><score>9.4</score>
<pdfVersion>1.4</pdfVersion>
<pdfPageSize>612 x 794 pts</pdfPageSize>
<refBibsNative>false</refBibsNative>
<keywordCount>1</keywordCount>
<abstractCharCount>1298</abstractCharCount>
<pdfWordCount>7183</pdfWordCount>
<pdfCharCount>58043</pdfCharCount>
<pdfPageCount>13</pdfPageCount>
<abstractWordCount>200</abstractWordCount>
</qualityIndicators>
<title>Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
<refBibs><json:item><author><json:item><name>D Hanahan</name>
</json:item>
<json:item><name>R,A Weinberg</name>
</json:item>
</author>
<host><volume>100</volume>
<pages><last>70</last>
<first>57</first>
</pages>
<author></author>
<title>Cell</title>
<publicationDate>2000</publicationDate>
</host>
<title>The hallmarks of cancer</title>
<publicationDate>2000</publicationDate>
</json:item>
<json:item><author><json:item><name>A Jemal</name>
</json:item>
<json:item><name>T Murray</name>
</json:item>
<json:item><name>A Samuels</name>
</json:item>
<json:item><name>A Ghafoor</name>
</json:item>
<json:item><name>E Ward</name>
</json:item>
<json:item><name>M,J Thun</name>
</json:item>
</author>
<host><volume>53</volume>
<pages><last>26</last>
<first>5</first>
</pages>
<author></author>
<title>CA Cancer J. Clin</title>
<publicationDate>2003</publicationDate>
</host>
<title>Cancer statistics</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>J,C Venter</name>
</json:item>
<json:item><name>M,D Adams</name>
</json:item>
<json:item><name>E,W Myers</name>
</json:item>
<json:item><name>P,W Li</name>
</json:item>
<json:item><name>R,J Mural</name>
</json:item>
<json:item><name>G,G Sutton</name>
</json:item>
<json:item><name>H,O Smith</name>
</json:item>
<json:item><name>M Yandell</name>
</json:item>
<json:item><name>C,A Evans</name>
</json:item>
<json:item><name>R,A Holt</name>
</json:item>
</author>
<host><volume>291</volume>
<pages><last>1351</last>
<first>1304</first>
</pages>
<author></author>
<title>Science</title>
<publicationDate>2001</publicationDate>
</host>
<title>The sequence of the human genome</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>S Ramaswamy</name>
</json:item>
<json:item><name>T,R Golub</name>
</json:item>
</author>
<host><volume>20</volume>
<pages><last>1941</last>
<first>1932</first>
</pages>
<author></author>
<title>J. Clin. Oncol</title>
<publicationDate>2002</publicationDate>
</host>
<title>DNA microarrays in clinical oncology</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>S,C Geller</name>
</json:item>
<json:item><name>J,P Gregg</name>
</json:item>
<json:item><name>P Hagerman</name>
</json:item>
<json:item><name>D,M Rocke</name>
</json:item>
</author>
<host><volume>19</volume>
<pages><last>1823</last>
<first>1817</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2003</publicationDate>
</host>
<title>Transformation and normalization of oligonucleotide microarray data</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>R Hoffmann</name>
</json:item>
<json:item><name>T Seidl</name>
</json:item>
<json:item><name>M Dugas</name>
</json:item>
</author>
<host><volume>3</volume>
<pages><first>0033</first>
</pages>
<author></author>
<title>Genome Biol</title>
<publicationDate>2002</publicationDate>
</host>
<title>Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>J Quackenbush</name>
</json:item>
</author>
<host><volume>32</volume>
<pages><last>501</last>
<first>496</first>
</pages>
<author></author>
<title>Nature Genet</title>
<publicationDate>2002</publicationDate>
</host>
<title>Microarray data normalization and transformation</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>A Zien</name>
</json:item>
<json:item><name>T Aigner</name>
</json:item>
<json:item><name>R Zimmer</name>
</json:item>
<json:item><name>T Lengauer</name>
</json:item>
</author>
<host><pages><last>323</last>
<first>17</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2001</publicationDate>
</host>
<title>Centralization: a new method for the normalization of gene expression data</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>L,M Cope</name>
</json:item>
<json:item><name>R,A Irizarry</name>
</json:item>
<json:item><name>H,A Jaffee</name>
</json:item>
<json:item><name>Z Wu</name>
</json:item>
<json:item><name>T,P Speed</name>
</json:item>
</author>
<host><volume>20</volume>
<pages><last>331</last>
<first>323</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2004</publicationDate>
</host>
<title>A benchmark for Affymetrix GeneChip expression measures</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>A Brazma</name>
</json:item>
<json:item><name>J Vilo</name>
</json:item>
</author>
<host><volume>3</volume>
<pages><last>829</last>
<first>823</first>
</pages>
<author></author>
<title>Microbes Infect</title>
<publicationDate>2001</publicationDate>
</host>
<title>Gene expression data analysis</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>P Krajewski</name>
</json:item>
<json:item><name>J Bocianowski</name>
</json:item>
</author>
<host><volume>43</volume>
<pages><last>278</last>
<first>269</first>
</pages>
<author></author>
<title>J. Appl. Genet</title>
<publicationDate>2002</publicationDate>
</host>
<title>Statistical methods for microarray assays</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>H Zhang</name>
</json:item>
<json:item><name>C,Y Yu</name>
</json:item>
<json:item><name>B Singer</name>
</json:item>
<json:item><name>M Xiong</name>
</json:item>
</author>
<host><pages><last>6735</last>
<first>6730</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>2001</publicationDate>
</host>
<title>Recursive partitioning for tumor classification with gene expression microarray data</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>J Theilhaber</name>
</json:item>
<json:item><name>S Bushnell</name>
</json:item>
<json:item><name>A Jackson</name>
</json:item>
<json:item><name>R Fuchs</name>
</json:item>
</author>
<host><volume>8</volume>
<pages><last>614</last>
<first>585</first>
</pages>
<author></author>
<title>J. Comput. Biol</title>
<publicationDate>2001</publicationDate>
</host>
<title>Bayesian estimation of fold-changes in the analysis of gene expression: the PFOLD algorithm</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>D Horn</name>
</json:item>
<json:item><name>I Axel</name>
</json:item>
</author>
<host><volume>19</volume>
<pages><last>1115</last>
<first>1110</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2003</publicationDate>
</host>
<title>Novel clustering algorithm for microarray expression data in a truncated SVD space</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>D,V Nguyen</name>
</json:item>
<json:item><name>D,M Rocke</name>
</json:item>
</author>
<host><volume>18</volume>
<pages><last>50</last>
<first>39</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2002</publicationDate>
</host>
<title>Tumor classification by partial least squares using microarray gene expression data</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>S,I Lee</name>
</json:item>
<json:item><name>S Batzoglou</name>
</json:item>
</author>
<host><volume>4</volume>
<pages><first>76</first>
</pages>
<author></author>
<title>Genome Biol</title>
<publicationDate>2003</publicationDate>
</host>
<title>Application of independent component analysis to microarrays</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>R,L Somorjai</name>
</json:item>
<json:item><name>B Dolenko</name>
</json:item>
<json:item><name>R Baumgartner</name>
</json:item>
</author>
<host><volume>19</volume>
<pages><last>1491</last>
<first>1484</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2003</publicationDate>
</host>
<title>Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>D Cora</name>
</json:item>
<json:item><name>Di Cunto</name>
</json:item>
<json:item><name>F Provero</name>
</json:item>
<json:item><name>P Silengo</name>
</json:item>
<json:item><name>L Caselle</name>
</json:item>
<json:item><name>M </name>
</json:item>
</author>
<host><volume>5</volume>
<pages><first>57</first>
</pages>
<author></author>
<title>BMC Bioinformatics</title>
<publicationDate>2004</publicationDate>
</host>
<title>Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>J,W Tullai</name>
</json:item>
<json:item><name>M,E Schaffer</name>
</json:item>
<json:item><name>S Mullenbrock</name>
</json:item>
<json:item><name>S Kasif</name>
</json:item>
<json:item><name>G,M Cooper</name>
</json:item>
</author>
<host><volume>279</volume>
<pages><last>20177</last>
<first>20167</first>
</pages>
<author></author>
<title>J. Biol. Chem</title>
<publicationDate>2004</publicationDate>
</host>
<title>Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>S Tavazoie</name>
</json:item>
<json:item><name>J,D Hughes</name>
</json:item>
<json:item><name>M,J Campbell</name>
</json:item>
<json:item><name>R,J Cho</name>
</json:item>
<json:item><name>G,M Church</name>
</json:item>
</author>
<host><volume>22</volume>
<pages><last>285</last>
<first>281</first>
</pages>
<author></author>
<title>Nature Genet</title>
<publicationDate>1999</publicationDate>
</host>
<title>Systematic determination of genetic network architecture</title>
<publicationDate>1999</publicationDate>
</json:item>
<json:item><author><json:item><name>X,S Liu</name>
</json:item>
<json:item><name>D,L Brutlag</name>
</json:item>
<json:item><name>J,S Liu</name>
</json:item>
</author>
<host><volume>20</volume>
<pages><last>839</last>
<first>835</first>
</pages>
<author></author>
<title>Nat. Biotechnol</title>
<publicationDate>2002</publicationDate>
</host>
<title>An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments</title>
<publicationDate>2002</publicationDate>
</json:item>
<json:item><author><json:item><name>J Zheng</name>
</json:item>
<json:item><name>J Wu</name>
</json:item>
<json:item><name>Z Sun</name>
</json:item>
</author>
<host><volume>31</volume>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>1995</publicationDate>
</host>
<title>An approach to identify over-represented cis-elements in related sequences</title>
<publicationDate>1995</publicationDate>
</json:item>
<json:item><author><json:item><name>H,J Bussemaker</name>
</json:item>
<json:item><name>H Li</name>
</json:item>
<json:item><name>E,D Siggia</name>
</json:item>
</author>
<host><volume>27</volume>
<pages><last>171</last>
<first>167</first>
</pages>
<author></author>
<title>Nature Genet</title>
<publicationDate>2001</publicationDate>
</host>
<title>Regulatory element detection using correlation with expression</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>E,M Conlon</name>
</json:item>
<json:item><name>X,S Liu</name>
</json:item>
<json:item><name>J,D Lieb</name>
</json:item>
<json:item><name>J,S Liu</name>
</json:item>
</author>
<host><pages><last>3344</last>
<first>3339</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>2003</publicationDate>
</host>
<title>Integrating regulatory motif discovery and genome-wide expression analysis</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>P Nitschke</name>
</json:item>
<json:item><name>P Guerdoux-Jamet</name>
</json:item>
<json:item><name>H Chiapello</name>
</json:item>
<json:item><name>G Faroux</name>
</json:item>
<json:item><name>C Henaut</name>
</json:item>
<json:item><name>A Henaut</name>
</json:item>
<json:item><name>A Danchin</name>
</json:item>
</author>
<host><volume>22</volume>
<pages><last>227</last>
<first>207</first>
</pages>
<author></author>
<title>FEMS Microbiol. Rev</title>
<publicationDate>1998</publicationDate>
</host>
<title>Indigo: a World-Wide-Web review of genomes and gene functions</title>
<publicationDate>1998</publicationDate>
</json:item>
<json:item><author><json:item><name>D Hernandez</name>
</json:item>
<json:item><name>R Gras</name>
</json:item>
<json:item><name>R Appel</name>
</json:item>
</author>
<host><volume>28</volume>
<pages><last>128</last>
<first>119</first>
</pages>
<author></author>
<title>Comput. Biol. Chem</title>
<publicationDate>2004</publicationDate>
</host>
<title>MoDEL: An efficient strategy for ungapped local multiple alignment</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>A Brazma</name>
</json:item>
<json:item><name>H Parkinson</name>
</json:item>
<json:item><name>U Sarkans</name>
</json:item>
<json:item><name>M Shojatalab</name>
</json:item>
<json:item><name>J Vilo</name>
</json:item>
<json:item><name>N Abeygunawardena</name>
</json:item>
<json:item><name>E Holloway</name>
</json:item>
<json:item><name>M Kapushesky</name>
</json:item>
<json:item><name>P Kemmeren</name>
</json:item>
<json:item><name>G,G Lara</name>
</json:item>
</author>
<host><volume>31</volume>
<pages><last>71</last>
<first>68</first>
</pages>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>2003</publicationDate>
</host>
<title>ArrayExpress—a public repository for microarray gene expression data at the EBI</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>P Rocca-Serra</name>
</json:item>
<json:item><name>A Brazma</name>
</json:item>
<json:item><name>H Parkinson</name>
</json:item>
<json:item><name>U Sarkans</name>
</json:item>
<json:item><name>M Shojatalab</name>
</json:item>
<json:item><name>S Contrino</name>
</json:item>
<json:item><name>J Vilo</name>
</json:item>
<json:item><name>N Abeygunawardena</name>
</json:item>
<json:item><name>G Mukherjee</name>
</json:item>
<json:item><name>E Holloway</name>
</json:item>
</author>
<host><volume>326</volume>
<pages><last>1078</last>
<first>1075</first>
</pages>
<author></author>
<title>C R Biol</title>
<publicationDate>2003</publicationDate>
</host>
<title>ArrayExpress: a public database of gene expression data at EBI</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>C Li</name>
</json:item>
<json:item><name>W Wong</name>
</json:item>
</author>
<host><pages><last>141</last>
<first>120</first>
</pages>
<author></author>
<title>The Analysis of Gene Expression Data: Methods and Software</title>
<publicationDate>2003</publicationDate>
</host>
<title>DNA-Chip Analyzer (dChip)</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>N Saitou</name>
</json:item>
<json:item><name>M Nei</name>
</json:item>
</author>
<host><volume>4</volume>
<pages><last>425</last>
<first>406</first>
</pages>
<author></author>
<title>Mol. Biol. Evol</title>
<publicationDate>1987</publicationDate>
</host>
<title>The neighbor-joining method: a new method for reconstructing phylogenetic trees</title>
<publicationDate>1987</publicationDate>
</json:item>
<json:item><author><json:item><name>S Kumar</name>
</json:item>
<json:item><name>K Tamura</name>
</json:item>
<json:item><name>I,B Jakobsen</name>
</json:item>
<json:item><name>M Nei</name>
</json:item>
</author>
<host><volume>17</volume>
<pages><last>1245</last>
<first>1244</first>
</pages>
<author></author>
<title>Bioinformatics</title>
<publicationDate>2001</publicationDate>
</host>
<title>MEGA2: molecular evolutionary genetics analysis software</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>J Aach</name>
</json:item>
<json:item><name>M,L Bulyk</name>
</json:item>
<json:item><name>G,M Church</name>
</json:item>
<json:item><name>J Comander</name>
</json:item>
<json:item><name>A Derti</name>
</json:item>
<json:item><name>J Shendure</name>
</json:item>
</author>
<host><volume>409</volume>
<pages><last>859</last>
<first>856</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>2001</publicationDate>
</host>
<title>Computational comparison of two draft sequences of the human genome</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>E,S Lander</name>
</json:item>
<json:item><name>L,M Linton</name>
</json:item>
<json:item><name>B Birren</name>
</json:item>
<json:item><name>C Nusbaum</name>
</json:item>
<json:item><name>M,C Zody</name>
</json:item>
<json:item><name>J Baldwin</name>
</json:item>
<json:item><name>K Devon</name>
</json:item>
<json:item><name>K Dewar</name>
</json:item>
<json:item><name>M Doyle</name>
</json:item>
<json:item><name>W Fitzhugh</name>
</json:item>
</author>
<host><volume>409</volume>
<pages><last>921</last>
<first>860</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>2001</publicationDate>
</host>
<title>Initial sequencing and analysis of the human genome</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>A Cravchik</name>
</json:item>
<json:item><name>G Subramanian</name>
</json:item>
<json:item><name>S Broder</name>
</json:item>
<json:item><name>J,C Venter</name>
</json:item>
</author>
<host><volume>58</volume>
<pages><last>1778</last>
<first>1772</first>
</pages>
<author></author>
<title>Arch. Neurol</title>
<publicationDate>2001</publicationDate>
</host>
<title>Sequence analysis of the human genome: implications for the understanding of nervous system function and disease</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>E Wingender</name>
</json:item>
</author>
<host><volume>4</volume>
<pages><last>61</last>
<first>55</first>
</pages>
<author></author>
<title>In Silico Biol</title>
<publicationDate>2004</publicationDate>
</host>
<title>TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>A,E Kel</name>
</json:item>
<json:item><name>E Gossling</name>
</json:item>
<json:item><name>I Reuter</name>
</json:item>
<json:item><name>E Cheremushkin</name>
</json:item>
<json:item><name>O,V Kel-Margoulis</name>
</json:item>
<json:item><name>E Wingender</name>
</json:item>
</author>
<host><volume>31</volume>
<pages><last>3579</last>
<first>3576</first>
</pages>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>2003</publicationDate>
</host>
<title>MATCH: A tool for searching transcription factor binding sites in DNA sequences</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>Y Yap</name>
</json:item>
<json:item><name>X Zhang</name>
</json:item>
<json:item><name>M Ling</name>
</json:item>
<json:item><name>X Wang</name>
</json:item>
<json:item><name>Y Wong</name>
</json:item>
<json:item><name>A Danchin</name>
</json:item>
</author>
<host><volume>4</volume>
<pages><first>72</first>
</pages>
<author></author>
<title>BMC Cancer</title>
<publicationDate>2004</publicationDate>
</host>
<title>Classification between normal and tumor tissues based on the pair-wise gene expression ratio</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><host><author><json:item><name>D,G Beer</name>
</json:item>
<json:item><name>S,L Kardia</name>
</json:item>
<json:item><name>C,C Huang</name>
</json:item>
<json:item><name>T,J Giordano</name>
</json:item>
<json:item><name>A,M Levin</name>
</json:item>
</author>
</host>
</json:item>
<json:item><author></author>
<host><volume>8</volume>
<pages><last>824</last>
<first>816</first>
</pages>
<author></author>
<title>Nature Med</title>
</host>
<title>Gene-expression profiles predict survival of patients with lung adenocarcinoma</title>
</json:item>
<json:item><author><json:item><name>A Bhattacharjee</name>
</json:item>
<json:item><name>W,G Richards</name>
</json:item>
<json:item><name>J Staunton</name>
</json:item>
<json:item><name>C Li</name>
</json:item>
<json:item><name>S Monti</name>
</json:item>
<json:item><name>P Vasa</name>
</json:item>
<json:item><name>C Ladd</name>
</json:item>
<json:item><name>J Beheshti</name>
</json:item>
<json:item><name>R Bueno</name>
</json:item>
<json:item><name>M Gillette</name>
</json:item>
</author>
<host><pages><last>13795</last>
<first>13790</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>2001</publicationDate>
</host>
<title>Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>P Fardin</name>
</json:item>
<json:item><name>J Bahler</name>
</json:item>
<json:item><name>P Capanni</name>
</json:item>
<json:item><name>E Inglese</name>
</json:item>
<json:item><name>A Ricciardi</name>
</json:item>
<json:item><name>G,B Ferrara</name>
</json:item>
</author>
<host><volume>64</volume>
<pages><first>116</first>
</pages>
<author></author>
<title>Hum. Immunol</title>
<publicationDate>2003</publicationDate>
</host>
<title>Gene expression analysis in non small cell lung cancer (NSCLC) using microarray technology</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><host><author><json:item><name>O Warburg</name>
</json:item>
</author>
<title>The Metabolism of Tumours</title>
<publicationDate>1930</publicationDate>
</host>
</json:item>
<json:item><author><json:item><name>A Goel</name>
</json:item>
<json:item><name>S,P Mathupala</name>
</json:item>
<json:item><name>P,L Pedersen</name>
</json:item>
</author>
<host><volume>278</volume>
<pages><last>15340</last>
<first>15333</first>
</pages>
<author></author>
<title>J. Biol. Chem</title>
<publicationDate>2003</publicationDate>
</host>
<title>Glucose metabolism in cancer. Evidence that demethylation events play a role in activating type II hexokinase gene expression</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>M,G Lee</name>
</json:item>
<json:item><name>P,L Pedersen</name>
</json:item>
</author>
<host><volume>278</volume>
<pages><last>41058</last>
<first>41047</first>
</pages>
<author></author>
<title>J. Biol. Chem</title>
<publicationDate>2003</publicationDate>
</host>
<title>Glucose metabolism in cancer: importance of transcription factor-DNA interactions within a short segment of the proximal region of the type II hexokinase promoter</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>P Carmeliet</name>
</json:item>
<json:item><name>Y Dor</name>
</json:item>
<json:item><name>J,M Herbert</name>
</json:item>
<json:item><name>D Fukumura</name>
</json:item>
<json:item><name>K Brusselmans</name>
</json:item>
<json:item><name>M Dewerchin</name>
</json:item>
<json:item><name>M Neeman</name>
</json:item>
<json:item><name>F Bono</name>
</json:item>
<json:item><name>R Abramovitch</name>
</json:item>
<json:item><name>P Maxwell</name>
</json:item>
</author>
<host><volume>394</volume>
<pages><last>490</last>
<first>485</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>1998</publicationDate>
</host>
<title>Role of HIF-1alpha in hypoxia-mediated apoptosis, cell proliferation and tumour angiogenesis</title>
<publicationDate>1998</publicationDate>
</json:item>
<json:item><author><json:item><name>W,G An</name>
</json:item>
<json:item><name>M Kanekal</name>
</json:item>
<json:item><name>M,C Simon</name>
</json:item>
<json:item><name>E Maltepe</name>
</json:item>
<json:item><name>M,V Blagosklonny</name>
</json:item>
<json:item><name>L,M Neckers</name>
</json:item>
</author>
<host><volume>392</volume>
<pages><last>408</last>
<first>405</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>1998</publicationDate>
</host>
<title>Stabilization of wild-type p53 by hypoxia-inducible factor 1alpha</title>
<publicationDate>1998</publicationDate>
</json:item>
<json:item><author><json:item><name>S,P Mathupala</name>
</json:item>
<json:item><name>C Heese</name>
</json:item>
<json:item><name>P,L Pedersen</name>
</json:item>
</author>
<host><volume>272</volume>
<pages><last>22780</last>
<first>22776</first>
</pages>
<author></author>
<title>J. Biol. Chem</title>
<publicationDate>1997</publicationDate>
</host>
<title>Glucose catabolism in cancer cells. The type II hexokinase promoter contains functionally active response elements for the tumor suppressor p53</title>
<publicationDate>1997</publicationDate>
</json:item>
<json:item><author><json:item><name>A Rempel</name>
</json:item>
<json:item><name>S,P Mathupala</name>
</json:item>
<json:item><name>C,A Griffin</name>
</json:item>
<json:item><name>A,L Hawkins</name>
</json:item>
<json:item><name>P,L Pedersen</name>
</json:item>
</author>
<host><volume>56</volume>
<pages><last>2471</last>
<first>2468</first>
</pages>
<author></author>
<title>Cancer Res</title>
<publicationDate>1996</publicationDate>
</host>
<title>Glucose catabolism in cancer cells: amplification of the gene encoding type II hexokinase</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>J,R Gnarra</name>
</json:item>
<json:item><name>S Zhou</name>
</json:item>
<json:item><name>M,J Merrill</name>
</json:item>
<json:item><name>J,R Wagner</name>
</json:item>
<json:item><name>A Krumm</name>
</json:item>
<json:item><name>E Papavassiliou</name>
</json:item>
<json:item><name>E,H Oldfield</name>
</json:item>
<json:item><name>R,D Klausner</name>
</json:item>
<json:item><name>W,M Linehan</name>
</json:item>
</author>
<host><pages><last>10594</last>
<first>10589</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>1996</publicationDate>
</host>
<title>Post-transcriptional regulation of vascular endothelial growth factor mRNA by the product of the VHL tumor suppressor gene</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>B,C Lewis</name>
</json:item>
<json:item><name>H Shim</name>
</json:item>
<json:item><name>Q Li</name>
</json:item>
<json:item><name>C,S Wu</name>
</json:item>
<json:item><name>L,A Lee</name>
</json:item>
<json:item><name>A Maity</name>
</json:item>
<json:item><name>C,V Dang</name>
</json:item>
</author>
<host><volume>17</volume>
<pages><last>4978</last>
<first>4967</first>
</pages>
<author></author>
<title>Mol. Cell. Biol</title>
<publicationDate>1997</publicationDate>
</host>
<title>Identification of putative c-Myc-responsive genes: characterization of rcl, a novel growth-related gene</title>
<publicationDate>1997</publicationDate>
</json:item>
<json:item><author><json:item><name>Y Akiyama</name>
</json:item>
<json:item><name>T Hosoya</name>
</json:item>
<json:item><name>A,M Poole</name>
</json:item>
<json:item><name>Y Hotta</name>
</json:item>
</author>
<host><pages><last>14916</last>
<first>14912</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>1996</publicationDate>
</host>
<title>The gcm-motif: a novel DNA-binding motif conserved in Drosophila and mammals</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>E,S Liu</name>
</json:item>
<json:item><name>A,S Lee</name>
</json:item>
</author>
<host><volume>19</volume>
<pages><last>5431</last>
<first>5425</first>
</pages>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>1991</publicationDate>
</host>
<title>Common sets of nuclear factors binding to the conserved promoter sequence motif of two coordinately regulated ER protein genes, GRP78 and GRP94</title>
<publicationDate>1991</publicationDate>
</json:item>
<json:item><author><json:item><name>H Singh</name>
</json:item>
<json:item><name>R Sen</name>
</json:item>
<json:item><name>D Baltimore</name>
</json:item>
<json:item><name>P,A Sharp</name>
</json:item>
</author>
<host><volume>319</volume>
<pages><last>158</last>
<first>154</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>1986</publicationDate>
</host>
<title>A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes</title>
<publicationDate>1986</publicationDate>
</json:item>
<json:item><author><json:item><name>H Siomi</name>
</json:item>
<json:item><name>M,J Matunis</name>
</json:item>
<json:item><name>W,M Michael</name>
</json:item>
<json:item><name>G Dreyfuss</name>
</json:item>
</author>
<host><volume>21</volume>
<pages><last>1198</last>
<first>1193</first>
</pages>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>1993</publicationDate>
</host>
<title>The pre-mRNA binding K protein contains a novel evolutionarily conserved motif</title>
<publicationDate>1993</publicationDate>
</json:item>
<json:item><author><json:item><name>S,M Srinivasula</name>
</json:item>
<json:item><name>R Hegde</name>
</json:item>
<json:item><name>A Saleh</name>
</json:item>
<json:item><name>P Datta</name>
</json:item>
<json:item><name>E Shiozaki</name>
</json:item>
<json:item><name>J Chai</name>
</json:item>
<json:item><name>R,A Lee</name>
</json:item>
<json:item><name>P,D Robbins</name>
</json:item>
<json:item><name>T Fernandes-Alnemri</name>
</json:item>
<json:item><name>Y Shi</name>
</json:item>
</author>
<host><volume>410</volume>
<pages><last>116</last>
<first>112</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>2001</publicationDate>
</host>
<title>A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO regulates caspase activity and apoptosis</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>W,W Wasserman</name>
</json:item>
<json:item><name>M Palumbo</name>
</json:item>
<json:item><name>W Thompson</name>
</json:item>
<json:item><name>J,W Fickett</name>
</json:item>
<json:item><name>C,E Lawrence</name>
</json:item>
</author>
<host><volume>26</volume>
<pages><last>228</last>
<first>225</first>
</pages>
<author></author>
<title>Nature Genet</title>
<publicationDate>2000</publicationDate>
</host>
<title>Human-mouse genome comparisons to locate regulatory sites</title>
<publicationDate>2000</publicationDate>
</json:item>
<json:item><author><json:item><name>J,W Fickett</name>
</json:item>
<json:item><name>A,G Hatzigeorgiou</name>
</json:item>
</author>
<host><volume>7</volume>
<pages><last>878</last>
<first>861</first>
</pages>
<author></author>
<title>Genome Res</title>
<publicationDate>1997</publicationDate>
</host>
<title>Eukaryotic promoter recognition</title>
<publicationDate>1997</publicationDate>
</json:item>
<json:item><author><json:item><name>J,M Claverie</name>
</json:item>
<json:item><name>S Audic</name>
</json:item>
</author>
<host><volume>12</volume>
<pages><last>439</last>
<first>431</first>
</pages>
<author></author>
<title>Comput. Appl. Biosci</title>
<publicationDate>1996</publicationDate>
</host>
<title>The statistical significance of nucleotide position-weight matrix matches</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>L,M Jakt</name>
</json:item>
<json:item><name>L Cao</name>
</json:item>
<json:item><name>K,S Cheah</name>
</json:item>
<json:item><name>D,K Smith</name>
</json:item>
</author>
<host><volume>11</volume>
<pages><last>123</last>
<first>112</first>
</pages>
<author></author>
<title>Genome Res</title>
<publicationDate>2001</publicationDate>
</host>
<title>Assessing clusters and motifs from gene expression data</title>
<publicationDate>2001</publicationDate>
</json:item>
<json:item><author><json:item><name>G Gosset</name>
</json:item>
<json:item><name>Z Zhang</name>
</json:item>
<json:item><name>S Nayyar</name>
</json:item>
<json:item><name>W,A Cuevas</name>
</json:item>
<json:item><name>M,H Saier</name>
</json:item>
<json:item><name> Jr</name>
</json:item>
</author>
<host><volume>186</volume>
<pages><last>3524</last>
<first>3516</first>
</pages>
<author></author>
<title>J. Bacteriol</title>
<publicationDate>2004</publicationDate>
</host>
<title>Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>B Magasanik</name>
</json:item>
<json:item><name>F,C Neidhardt</name>
</json:item>
</author>
<host><volume>2</volume>
<pages><last>1325</last>
<first>1318</first>
</pages>
<author></author>
<title>Cellular and Molecular Biology</title>
<publicationDate>1987</publicationDate>
</host>
<title>Regulation of carbon and nitrogen utilization. Escherichia coli and Salmonella typhimurium</title>
<publicationDate>1987</publicationDate>
</json:item>
<json:item><author><json:item><name>C,D Trainor</name>
</json:item>
<json:item><name>T Evans</name>
</json:item>
<json:item><name>G Felsenfeld</name>
</json:item>
<json:item><name>M,S Boguski</name>
</json:item>
</author>
<host><volume>343</volume>
<pages><last>96</last>
<first>92</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>1990</publicationDate>
</host>
<title>Structure and evolution of a human erythroid transcription factor</title>
<publicationDate>1990</publicationDate>
</json:item>
<json:item><author><json:item><name>Z Duan</name>
</json:item>
<json:item><name>M Horwitz</name>
</json:item>
</author>
<host><pages><last>5937</last>
<first>5932</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>2003</publicationDate>
</host>
<title>Targets of the transcriptional repressor oncoprotein Gfi-1</title>
<publicationDate>2003</publicationDate>
</json:item>
<json:item><author><json:item><name>J Van Helden</name>
</json:item>
<json:item><name>B Andre</name>
</json:item>
<json:item><name>J Collado-Vides</name>
</json:item>
</author>
<host><volume>281</volume>
<pages><last>842</last>
<first>827</first>
</pages>
<author></author>
<title>J. Mol. Biol</title>
<publicationDate>1998</publicationDate>
</host>
<title>Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies</title>
<publicationDate>1998</publicationDate>
</json:item>
<json:item><author><json:item><name>L,E Huang</name>
</json:item>
<json:item><name>J Gu</name>
</json:item>
<json:item><name>M Schau</name>
</json:item>
<json:item><name>H,F Bunn</name>
</json:item>
</author>
<host><pages><last>7992</last>
<first>7987</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>1998</publicationDate>
</host>
<title>Regulation of hypoxia-inducible factor 1alpha is mediated by an O2-dependent degradation domain via the ubiquitin-proteasome pathway</title>
<publicationDate>1998</publicationDate>
</json:item>
<json:item><author><json:item><name>D,E Swinson</name>
</json:item>
<json:item><name>J,L Jones</name>
</json:item>
<json:item><name>G Cox</name>
</json:item>
<json:item><name>D Richardson</name>
</json:item>
<json:item><name>A,L Harris</name>
</json:item>
<json:item><name>O Byrne</name>
</json:item>
<json:item><name>K,J </name>
</json:item>
</author>
<host><volume>111</volume>
<pages><last>50</last>
<first>43</first>
</pages>
<author></author>
<title>Int. J. Cancer</title>
<publicationDate>2004</publicationDate>
</host>
<title>Hypoxia-inducible factor-1alpha in non small cell lung cancer: relation to growth factor, protease and apoptosis pathways</title>
<publicationDate>2004</publicationDate>
</json:item>
<json:item><author><json:item><name>P,A Zweidler-Mckay</name>
</json:item>
<json:item><name>H,L Grimes</name>
</json:item>
<json:item><name>M,M Flubacher</name>
</json:item>
<json:item><name>P,N Tsichlis</name>
</json:item>
</author>
<host><volume>16</volume>
<pages><last>4034</last>
<first>4024</first>
</pages>
<author></author>
<title>Mol. Cell. Biol</title>
<publicationDate>1996</publicationDate>
</host>
<title>Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>H,L Grimes</name>
</json:item>
<json:item><name>C,B Gilks</name>
</json:item>
<json:item><name>T,O Chan</name>
</json:item>
<json:item><name>S Porter</name>
</json:item>
<json:item><name>P,N Tsichlis</name>
</json:item>
</author>
<host><pages><last>14573</last>
<first>14569</first>
</pages>
<author></author>
<title>Proc. Natl Acad. Sci. USA</title>
<publicationDate>1996</publicationDate>
</host>
<title>The Gfi-1 protooncoprotein represses Bax expression and inhibits T-cell death</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>D Wotton</name>
</json:item>
<json:item><name>R,S Lo</name>
</json:item>
<json:item><name>S Lee</name>
</json:item>
<json:item><name>J Massague</name>
</json:item>
</author>
<host><volume>97</volume>
<pages><last>39</last>
<first>29</first>
</pages>
<author></author>
<title>Cell</title>
<publicationDate>1999</publicationDate>
</host>
<title>A Smad transcriptional corepressor</title>
<publicationDate>1999</publicationDate>
</json:item>
<json:item><author><json:item><name>K Eppert</name>
</json:item>
<json:item><name>S,W Scherer</name>
</json:item>
<json:item><name>H Ozcelik</name>
</json:item>
<json:item><name>R Pirone</name>
</json:item>
<json:item><name>P Hoodless</name>
</json:item>
<json:item><name>H Kim</name>
</json:item>
<json:item><name>L,C Tsui</name>
</json:item>
<json:item><name>B Bapat</name>
</json:item>
<json:item><name>S Gallinger</name>
</json:item>
<json:item><name>I,L Andrulis</name>
</json:item>
</author>
<host><volume>86</volume>
<pages><last>552</last>
<first>543</first>
</pages>
<author></author>
<title>Cell</title>
<publicationDate>1996</publicationDate>
</host>
<title>MADR2 maps to 18q21 and encodes a TGFbeta-regulated MAD-related protein that is functionally mutated in colorectal carcinoma</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>G Lagna</name>
</json:item>
<json:item><name>A Hata</name>
</json:item>
<json:item><name>A Hemmati-Brivanlou</name>
</json:item>
<json:item><name>J Massague</name>
</json:item>
</author>
<host><volume>383</volume>
<pages><last>836</last>
<first>832</first>
</pages>
<author></author>
<title>Nature</title>
<publicationDate>1996</publicationDate>
</host>
<title>Partnership between DPC4 and SMAD proteins in TGF-beta signalling pathways</title>
<publicationDate>1996</publicationDate>
</json:item>
<json:item><author><json:item><name>E Bertolino</name>
</json:item>
<json:item><name>B Reimund</name>
</json:item>
<json:item><name>D Wildt-Perinic</name>
</json:item>
<json:item><name>R,G Clerc</name>
</json:item>
</author>
<host><volume>270</volume>
<pages><last>31188</last>
<first>31178</first>
</pages>
<author></author>
<title>J. Biol. Chem</title>
<publicationDate>1995</publicationDate>
</host>
<title>A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif</title>
<publicationDate>1995</publicationDate>
</json:item>
<json:item><author><json:item><name>S,H Orkin</name>
</json:item>
</author>
<host><volume>63</volume>
<pages><last>672</last>
<first>665</first>
</pages>
<author></author>
<title>Cell</title>
<publicationDate>1990</publicationDate>
</host>
<title>Globin gene regulation and switching: circa 1990</title>
<publicationDate>1990</publicationDate>
</json:item>
<json:item><author><json:item><name>V Matys</name>
</json:item>
<json:item><name>E Fricke</name>
</json:item>
<json:item><name>R Geffers</name>
</json:item>
<json:item><name>E Gossling</name>
</json:item>
<json:item><name>M Haubrock</name>
</json:item>
<json:item><name>R Hehl</name>
</json:item>
<json:item><name>K Hornischer</name>
</json:item>
<json:item><name>D Karas</name>
</json:item>
<json:item><name>A,E Kel</name>
</json:item>
</author>
<host><volume>31</volume>
<pages><last>378</last>
<first>374</first>
</pages>
<author></author>
<title>Nucleic Acids Res</title>
<publicationDate>2003</publicationDate>
</host>
<title>TRANSFAC: transcriptional regulation, from patterns to profiles</title>
<publicationDate>2003</publicationDate>
</json:item>
</refBibs>
<genre><json:string>other</json:string>
</genre>
<host><volume>33</volume>
<publisherId><json:string>nar</json:string>
</publisherId>
<pages><last>421</last>
<first>409</first>
</pages>
<issn><json:string>0305-1048</json:string>
</issn>
<issue>1</issue>
<genre><json:string>journal</json:string>
</genre>
<language><json:string>unknown</json:string>
</language>
<eissn><json:string>1362-4962</json:string>
</eissn>
<title>Nucleic Acids Research</title>
</host>
<categories><wos><json:string>science</json:string>
<json:string>biochemistry & molecular biology</json:string>
</wos>
<scienceMetrix><json:string>health sciences</json:string>
<json:string>biomedical research</json:string>
<json:string>developmental biology</json:string>
</scienceMetrix>
</categories>
<publicationDate>2005</publicationDate>
<copyrightDate>2005</copyrightDate>
<doi><json:string>10.1093/nar/gki188</json:string>
</doi>
<id>0BFC1DB5DBE0149707002F146869EB08D51A995C</id>
<score>0.12236476</score>
<fulltext><json:item><extension>pdf</extension>
<original>true</original>
<mimetype>application/pdf</mimetype>
<uri>https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/fulltext/pdf</uri>
</json:item>
<json:item><extension>zip</extension>
<original>false</original>
<mimetype>application/zip</mimetype>
<uri>https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/fulltext/zip</uri>
</json:item>
<istex:fulltextTEI uri="https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
<respStmt><resp>Références bibliographiques récupérées via GROBID</resp>
<name resp="ISTEX-API">ISTEX-API (INIST-CNRS)</name>
</respStmt>
</titleStmt>
<publicationStmt><authority>ISTEX</authority>
<publisher>Oxford University Press</publisher>
<availability><p>© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org.</p>
</availability>
<date>2005</date>
</publicationStmt>
<notesStmt><note>*To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</note>
</notesStmt>
<sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
<author xml:id="author-1"><persName><forename type="first">Yee Leng</forename>
<surname>Yap</surname>
</persName>
<affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</affiliation>
<affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</affiliation>
<affiliation>To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</affiliation>
</author>
<author xml:id="author-2"><persName><forename type="first">Maria P.</forename>
<surname>Wong</surname>
</persName>
<affiliation>Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China</affiliation>
</author>
<author xml:id="author-3"><persName><forename type="first">Xue Wu</forename>
<surname>Zhang</surname>
</persName>
<affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</affiliation>
</author>
<author xml:id="author-4"><persName><forename type="first">David</forename>
<surname>Hernandez</surname>
</persName>
<affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</affiliation>
</author>
<author xml:id="author-5"><persName><forename type="first">Robin</forename>
<surname>Gras</surname>
</persName>
<affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</affiliation>
</author>
<author xml:id="author-6"><persName><forename type="first">David K.</forename>
<surname>Smith</surname>
</persName>
<affiliation>Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China</affiliation>
</author>
<author xml:id="author-7"><persName><forename type="first">Antoine</forename>
<surname>Danchin</surname>
</persName>
<affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</affiliation>
</author>
</analytic>
<monogr><title level="j">Nucleic Acids Research</title>
<title level="j" type="abbrev">Nucl. Acids Res.</title>
<idno type="pISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><publisher>Oxford University Press</publisher>
<date type="published" when="2005"></date>
<biblScope unit="volume">33</biblScope>
<biblScope unit="issue">1</biblScope>
<biblScope unit="page" from="409">409</biblScope>
<biblScope unit="page" to="421">421</biblScope>
</imprint>
</monogr>
<idno type="istex">0BFC1DB5DBE0149707002F146869EB08D51A995C</idno>
<idno type="DOI">10.1093/nar/gki188</idno>
<idno type="local">gki188</idno>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><creation><date>2005</date>
</creation>
<langUsage><language ident="en">en</language>
</langUsage>
<abstract xml:lang="en"><p>Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.</p>
</abstract>
<textClass><keywords scheme="keyword"><list><head>hwp-journal-coll</head>
<item><term>24</term>
</item>
</list>
</keywords>
</textClass>
</profileDesc>
<revisionDesc><change when="2005">Published</change>
<change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-12-22">References added</change>
</revisionDesc>
</teiHeader>
</istex:fulltextTEI>
<json:item><extension>txt</extension>
<original>false</original>
<mimetype>text/plain</mimetype>
<uri>https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/fulltext/txt</uri>
</json:item>
</fulltext>
<metadata><istex:metadataXml wicri:clean="corpus oup" 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">nar</journal-id>
<journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="publisher-id">nar</journal-id>
<journal-title>Nucleic Acids Research</journal-title>
<abbrev-journal-title abbrev-type="publisher">Nucl. Acids Res.</abbrev-journal-title>
<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="other">gki188</article-id>
<article-id pub-id-type="doi">10.1093/nar/gki188</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
<subj-group subj-group-type="hwp-journal-coll"><subject>24</subject>
</subj-group>
</article-categories>
<title-group><article-title>Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Yap</surname>
<given-names>Yee Leng</given-names>
</name>
<xref rid="AU1">1</xref>
<xref rid="AU2">2</xref>
<xref rid="COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wong</surname>
<given-names>Maria P.</given-names>
</name>
<xref rid="AU3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zhang</surname>
<given-names>Xue Wu</given-names>
</name>
<xref rid="AU1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hernandez</surname>
<given-names>David</given-names>
</name>
<xref rid="AU4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gras</surname>
<given-names>Robin</given-names>
</name>
<xref rid="AU4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Smith</surname>
<given-names>David K.</given-names>
</name>
<xref rid="AU5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Danchin</surname>
<given-names>Antoine</given-names>
</name>
<xref rid="AU2">2</xref>
</contrib>
<aff id="AU1"><sup>1</sup>
HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China </aff>
<aff id="AU2"><sup>2</sup>
Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France </aff>
<aff id="AU3"><sup>3</sup>
Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China </aff>
<aff id="AU4"><sup>4</sup>
Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland </aff>
<aff id="AU5"><sup>5</sup>
Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China </aff>
</contrib-group>
<author-notes><corresp id="COR1"><sup>*</sup>
To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: <ext-link xlink:href="daniely@hkusua.hku.hk" ext-link-type="email">daniely@hkusua.hku.hk</ext-link>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><year>2005</year>
</pub-date>
<volume>33</volume>
<issue>1</issue>
<fpage>409</fpage>
<lpage>421</lpage>
<history><date date-type="accepted"><day>12</day>
<month>12</month>
<year>2004</year>
</date>
<date date-type="received"><day>14</day>
<month>8</month>
<year>2004</year>
</date>
<date date-type="rev-recd"><day>02</day>
<month>11</month>
<year>2004</year>
</date>
</history>
<permissions><copyright-statement>© 2005, the authors <italic>Nucleic Acids Research, Vol. 33 No. 1</italic>
© <italic>Oxford University Press 2005; all rights reserved</italic>
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact <ext-link xlink:href="journals.permissions@oupjournals.org" ext-link-type="email">journals.permissions@oupjournals.org</ext-link>
.</copyright-statement>
<copyright-year>2005</copyright-year>
<license license-type="open-access"><p></p>
</license>
</permissions>
<abstract xml:lang="en"><p>Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set <italic>M</italic>
<sub>AD</sub>
, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside <italic>M</italic>
<sub>AD</sub>
. Terms that were overrepresented in <italic>M</italic>
<sub>AD</sub>
included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in <italic>M</italic>
<sub>AD</sub>
were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.</p>
</abstract>
<custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name>
<meta-value>409</meta-value>
</custom-meta>
<custom-meta><meta-name>hwp-legacy-dochead</meta-name>
<meta-value>research-article</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
</article>
</istex:document>
</istex:metadataXml>
<mods version="3.6"><titleInfo lang="en"><title>Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
</titleInfo>
<titleInfo type="alternative" lang="en" contentType="CDATA"><title>Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays</title>
</titleInfo>
<name type="personal"><namePart type="given">Yee Leng</namePart>
<namePart type="family">Yap</namePart>
<affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</affiliation>
<affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</affiliation>
<affiliation>To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Maria P.</namePart>
<namePart type="family">Wong</namePart>
<affiliation>Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Xue Wu</namePart>
<namePart type="family">Zhang</namePart>
<affiliation>HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">David</namePart>
<namePart type="family">Hernandez</namePart>
<affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Robin</namePart>
<namePart type="family">Gras</namePart>
<affiliation>Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">David K.</namePart>
<namePart type="family">Smith</namePart>
<affiliation>Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Antoine</namePart>
<namePart type="family">Danchin</namePart>
<affiliation>Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<typeOfResource>text</typeOfResource>
<genre type="other" displayLabel="other"></genre>
<subject><genre>hwp-journal-coll</genre>
<topic>24</topic>
</subject>
<originInfo><publisher>Oxford University Press</publisher>
<dateIssued encoding="w3cdtf">2005</dateIssued>
<copyrightDate encoding="w3cdtf">2005</copyrightDate>
</originInfo>
<language><languageTerm type="code" authority="iso639-2b">eng</languageTerm>
<languageTerm type="code" authority="rfc3066">en</languageTerm>
</language>
<physicalDescription><internetMediaType>text/html</internetMediaType>
</physicalDescription>
<abstract lang="en">Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.</abstract>
<note type="author-notes">*To whom correspondence should be addressed at HKU-Pasteur Research Centre, 8, Sassoon Road, Pokfulam, HongKong, China. Tel: +852 2816 8438; Fax: +852 2872 5782; Email: daniely@hkusua.hku.hk</note>
<relatedItem type="host"><titleInfo><title>Nucleic Acids Research</title>
</titleInfo>
<titleInfo type="abbreviated"><title>Nucl. Acids Res.</title>
</titleInfo>
<genre type="journal">journal</genre>
<identifier type="ISSN">0305-1048</identifier>
<identifier type="eISSN">1362-4962</identifier>
<identifier type="PublisherID">nar</identifier>
<identifier type="PublisherID-hwp">nar</identifier>
<identifier type="PublisherID-nlm-ta">Nucleic Acids Res</identifier>
<part><date>2005</date>
<detail type="volume"><caption>vol.</caption>
<number>33</number>
</detail>
<detail type="issue"><caption>no.</caption>
<number>1</number>
</detail>
<extent unit="pages"><start>409</start>
<end>421</end>
</extent>
</part>
</relatedItem>
<identifier type="istex">0BFC1DB5DBE0149707002F146869EB08D51A995C</identifier>
<identifier type="DOI">10.1093/nar/gki188</identifier>
<identifier type="local">gki188</identifier>
<accessCondition type="use and reproduction" contentType="copyright">© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org.</accessCondition>
<recordInfo><recordContentSource>OUP</recordContentSource>
</recordInfo>
</mods>
</metadata>
<annexes><json:item><extension>jpeg</extension>
<original>true</original>
<mimetype>image/jpeg</mimetype>
<uri>https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/annexes/jpeg</uri>
</json:item>
<json:item><extension>gif</extension>
<original>true</original>
<mimetype>image/gif</mimetype>
<uri>https://api.istex.fr/document/0BFC1DB5DBE0149707002F146869EB08D51A995C/annexes/gif</uri>
</json:item>
</annexes>
<serie></serie>
</istex>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/ParkinsonFranceV1/Data/Istex/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002341 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Corpus/biblio.hfd -nk 002341 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= ParkinsonFranceV1 |flux= Istex |étape= Corpus |type= RBID |clé= ISTEX:0BFC1DB5DBE0149707002F146869EB08D51A995C |texte= Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays }}
![]() | This area was generated with Dilib version V0.6.29. | ![]() |