Asa Ben-Hur

Publications (3)13.49 Total impact

• Article: CREME: Cis-Regulatory Module Explorer for the human genome.

  Roded Sharan, Asa Ben-Hur, Gabriela G Loots, Ivan Ovcharenko
  [show abstract] [hide abstract]
  ABSTRACT: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors whose binding sites are tightly clustered and form cis-regulatory modules. In this paper, we present a web server, CREME, for identifying and visualizing cis-regulatory modules in the promoter regions of a given set of potentially co-regulated genes. CREME relies on a database of putative transcription factor binding sites that have been annotated across the human genome using a library of position weight matrices and evolutionary conservation with the mouse and rat genomes. A search algorithm is applied to this data set to identify combinations of transcription factors whose binding sites tend to co-occur in close proximity in the promoter regions of the input gene set. The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web server is available at http://creme.dcode.org.
  Nucleic Acids Research 08/2004; 32(Web Server issue):W253-6. · 8.03 Impact Factor
• Article: Bioinformatics

  Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, M. Karp
  [show abstract] [hide abstract]
  ABSTRACT: Motivation: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of binding sites for transcription factors that cooperate in the regulation of genes. In this work we establish a framework for finding recurrent cisregulatory modules in the promoters of a selected set of genes and scoring their statistical significance.
  04/2003;
• Source

  Available from: oxfordjournals.org

  Article: CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.

  Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M Karp
  [show abstract] [hide abstract]
  ABSTRACT: MOTIVATION: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of binding sites for transcription factors that cooperate in the regulation of genes. In this work we establish a framework for finding recurrent cis-regulatory modules in the promoters of a selected set of genes and scoring their statistical significance. RESULTS: Proceeding from a database of identified binding site motifs and their genomic locations we seek motifs whose frequency in the selected promoters is different than in a background promoter set. We present several statistical tests designed for this purpose. We provide a hashing algorithm for detecting combinations of these motifs that co-occur in clusters within the selected promoters. The significance of such co-occurrences is evaluated using novel statistical scores. Our methods are combined in CREME, a suite of software which includes a browser for viewing the pattern of occurrence of selected cis-regulatory modules. We applied our methodology to find modules within human-mouse conserved promoter segments, focusing on cell cycle regulated genes and stress response related genes. To validate the biological significance of the identified modules we tested whether the associated genes tended to be co-expressed or share similar function. In the cell cycle set five of the seven identified sets of genes were coherently expressed. On the stress response data four of the six detected sets fell predominantly into well-defined functional sub-categories.
  Bioinformatics 02/2003; 19 Suppl 1:i283-91. · 5.47 Impact Factor