Computational prediction of novel components of lung transcriptional networks

Martinez, M. J., Smith, A. D., Li, B. L., Zhang, M. Q., Harrod, K. S. (January 2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics, 23 (1). pp. 21-29. ISSN 1367-4803

URL: https://www.ncbi.nlm.nih.gov/pubmed/17050569
DOI: 10.1093/bioinformatics/btl531

Abstract

Motivation: Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract. Results: Herein, a motif discovery approach was used to identify novel transcriptional regulators in the lung using genes previously found to be regulated by Foxa2 or Wnt signaling pathways. A human-mouse comparison of both novel and known motifs was also performed. Some of the factors and families identified here were previously shown to be involved epithelial cell differentiation (ETS family, HES-1 and MEIS-1), and ciliogenesis (RFX family), but have never been characterized in lung epithelia. Other unidentified over-represented motifs suggest the existence of novel mammalian lung transcription factors. Of the fraction of motifs examined we describe 25 transcription factor family predictions for lung. Fifteen novel factors were shown here to be expressed in mouse lung, and/or human bronchial or distal lung epithelial tissues or lung epithelial cell lineages.

Item Type: Paper
Uncontrolled Keywords: EPITHELIAL-CELL DIFFERENTIATION DNA-BINDING SPECIFICITY FORKHEAD PROTEINS NUCLEAR FACTOR GENE MODULES FACTOR-I MOUSE EXPRESSION FAMILY SITES
Subjects: bioinformatics > computational biology
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > epithelial cell
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > epithelial cell
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > epithelial cell

organs, tissues, organelles, cell types and functions > organs types and functions > lung
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: January 2007
Date Deposited: 09 Nov 2011 21:07
Last Modified: 02 Apr 2018 19:11
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23093

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