Fulltext

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays

Yap, Yee Leng ; Wong, Maria P. ; Zhang, Xue Wu ; Hernandez, David ; Gras, Robin ; Smith, David K. ; Danchin, Antoine

In: Nucleic Acids Research, 2005, vol. 33, no. 1, p. 409-421

Ajouter à la liste personnelle
    Titre
    • Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
    Auteur
    • Yap, Yee Leng. HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China
    • Wong, Maria P.. Department of Pathology, The University of Hong Kong Pokfulam, Hong Kong, China
    • Zhang, Xue Wu. HKU-Pasteur Research Centre Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong, China
    • Hernandez, David. Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland
    • Gras, Robin. Swiss Institute of Bioinformatics Proteome Informatics Group, CMU 1 Rue Michel-Servet CH 1211, Geneva 4, Switzerland
    • Smith, David K.. Department of Biochemistry, The University of Hong Kong Pokfulam, Hong Kong, China
    • Danchin, Antoine. Institute Pasteur, Unité de Génétique des Génomes Bactériens CNRS URA 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Nucleic Acids Research, 2005, vol. 33, no. 1, p. 409-421. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Mots clés
    Identifiant OAI-PMH
    • oai:doc.rero.ch:296008
    Summary
    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