Open Access Methodology article

Multivariate Hawkes process models of the occurrence of regulatory elements

Lisbeth Carstensen12, Albin Sandelin1, Ole Winther1 and Niels R Hansen2*

Author Affiliations

1 The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark

2 Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark

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BMC Bioinformatics 2010, 11:456  doi:10.1186/1471-2105-11-456

Published: 9 September 2010

Additional files

Additional file 1:

Mouse embryonic stem cell data - Part I. Coordinates of loci bound by Nanog, Oct4, Sox2, E2f1, Smad1, Zfx, c-myc, n-myc and Stat3.

Format: XLS Size: 7.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Mouse embryonic stem cell data - Part II. Coordinates of loci bound by p300 and Suz12.

Format: XLS Size: 324KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

ENCODE pilot data - hr00. Affymetrix ChIP-chip sites for the ENCODE pilot project to time hr00 with chromosome number, start position and end position for the enriched regions.

Format: ZIP Size: 102KB Download file

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Additional file 4:

ENCODE pilot data - hr02. Affymetrix ChIP-chip sites for the ENCODE pilot project to time hr02 with chromosome number, start position and end position for the enriched regions.

Format: ZIP Size: 67KB Download file

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Additional file 5:

ENCODE pilot data - hr08. Affymetrix ChIP-chip sites for the ENCODE pilot project to time hr08 with chromosome number, start position and end position for the enriched regions.

Format: ZIP Size: 96KB Download file

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Additional file 6:

ENCODE pilot data - hr32. Affymetrix ChIP-chip sites for the ENCODE pilot project to time hr32 with chromosome number, start position and end position for the enriched regions.

Format: ZIP Size: 62KB Download file

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Additional file 7:

ENCODE pilot data - The 44 pilot regions. The locations and names of the 44 ENCODE pilot regions.

Format: TXT Size: 1KB Download file

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Additional file 8:

Illustration of the occurrences of TREs in the ENCODE pilot regions. Illustration of the pilot ENCODE regions with the occurrences of the 10 TREs marked as point processes.

Format: PDF Size: 311KB Download file

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Additional file 9:

Information on installation of the R package ppstat. A PDF file of the web page for the R package ppstat (as of 12 August 2010) including information on installation.

Format: PDF Size: 48KB Download file

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Additional file 10:

Source code for the R package ppstat. Source code for the R package ppstat.

Format: GZ Size: 2.4MB Download file

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Additional file 11:

Note on the computations of the log-likelihood function. Note on the computations of the log-likelihood function and its first and second derivatives.

Format: PDF Size: 73KB Download file

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