Open Access Methodology article

Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite

Elena Y Harris2, Nadia Ponts1, Karine G Le Roch1* and Stefano Lonardi2*

Author Affiliations

1 Department of Cell Biology and Neuroscience, University of California, Riverside (CA) 92521 USA

2 Department of Computer Science and Engineering, University of California, Riverside (CA) 92521 USA

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BMC Genomics 2011, 12:601  doi:10.1186/1471-2164-12-601

Published: 13 December 2011

Additional files

Additional file 1:

File Additional_Table1.xls is an Excel spreadsheet. The list of 129 motifs identified by our method. Column A: ID of the FAIRE cluster for this motif Column B: k-mer that was used to find 1-mismatch (2-mismatch) neighborhood Column C: obtained by aligning the selected set of mutants for a motif Column D: another representation of the consensus of aligned mutants Column E: total number of mutants for a motif Column F: number mismatches allowed for a motif Column G: number of distinct genes, with occurrences of mutants within the functional windows (colors) Column H: total number of occurrences of mutants within functional windows of the target gene cluster Column I: total number of occurrences of mutants within 1000 bases promoters Column J: size of the target gene cluster (Note: color <= cluster size, because target gene cluster is selected for 1-mism neighborhood, but color is identified for the selected set of mutants that maximize HES) Column K: Hypergeometric Enrichment score (HES) = -log(p-value) Column L: HES in orthologous pbe Column M: HES in orthologous pch Column N: HES in orthologous pyo Column O: HES in orthologous pvivaxColumn P: Maximum value of pbe-hes, pch-hes, pyo-hes, pvivax-hes Column Q: Minimum p-values out of pbe, pch, pyo, pvivax (corresponding to max-ortholog HES), before correction for multiple testing Column R: Adjusted p-value corrected for multiple testing.

Format: XLSX Size: 28KB Download file

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