Research article
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
-
* Corresponding author: Martha L Bulyk mlbulyk@receptor.med.harvard.edu
1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
2 Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
3 Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
BMC Bioinformatics 2006, 7:229 doi:10.1186/1471-2105-7-229
Published: 27 April 2006Additional files
Additional file 1:
The following additional files are available with the online version of this paper, and also on the Bulyk lab website http://the_brain.bwh.harvard.edu webcite: a PDF file that shows the performance of MultiFinder with yeast ChIP-chip input set (Additional Figure 1); a PDF file that provides examples of motifs found by MultiFinder that failed the block filtering criteria (Additional Figure 2); a PDF file that provides heat maps of each of the 18 selected gene expression clusters that were examined with MultiFinder (Additional Figure 3); a PDF file that provides sample output from SequenceExtractor (Additional Figure 4); a text file in which we provide lists of the nonredundant RefSeq accession IDs to which we could map the Affymetrix probe IDs for each of these 18 expression clusters (Additional Data File 1); a text file in which we list the TRANSFAC TFBS matrix accession number and abbreviated motif name for each of 368 nonredundant vertebrate TFBS motifs (Additional Data File 2); a text file in which we describe the *.ace motif output files, *.svg graphical output files, and *.stat statistical files, available at http://the_brain.bwh.harvard.edu/GBMF webcite, for all known and novel motifs discovered by MultiFinder within the examined tissue-specific expression clusters, that passed our block filtering criteria and that had group specificity scores that were more significant than the geometric mean of the matched randoms, along with the geometric means and standard deviations of the group specificity scores for motifs resulting from the five sets size-matched randoms for each expression cluster (Additional Data File 3); a PDF file in which we provide tables supporting our word frequency analysis for each of nine different classes of genomic sequence windows from the human genome (Additional Table 1). In addition, on the Bulyk lab website http://the_brain.bwh.harvard.edu webcite, we provide via an academic license the MultiFinder, SequenceExtractor, and BlockFilter software and sample input and output files, and a PDF file in which we provide instructions for the installation and usage of the MultiFinder, SequenceExtractor and BlockFilter programs.
Format: PDF Size: 210KB Download file
This file can be viewed with: Adobe Acrobat Reader
