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PhyloScan: identification of transcription factor binding sites using cross-species evidence

Authors
  • C Steven Carmack
  • Lee Ann McCue
  • Lee A Newberg
  • Charles E Lawrence
Publisher
BioMed Central
Publication Date
Jan 23, 2007
Source
PMC
Keywords
Disciplines
  • Biology
License
Unknown

Abstract

SUPPLEMENTARY DATA Carmack, McCue, Newberg and Lawrence PhyloScan: Identification of transcription factor binding sites using cross-species evidence Algorithms for Molecular Biology, 2007 SUPPLEMENTARY DATA Supplementary Table 2 caption. The Excel data table lists the orthologs and the orthologous intergenic regions used in this study. Species abbreviations are: E. coli (ECOL), S. typhi (STYP), Y. pestis (YPES), H. influenzae (HINF), V. cholerae (VCHO), S. oneidensis (SONE), P. aeruginosa (PAER). For each E. coli gene, the common gene name and the upstream intergenic genomic coordinates are listed, followed by paired columns containing the orthologous information for each of the additional species, i.e., the name of the orthologous gene in each species and the corresponding upstream intergenic genomic coordinates. In cases where an ortholog of a particular E. coli gene was not present in a species, these columns contain a “-“. There were cases in which an orthologous gene was identified, but for which the upstream intergenic region was < 20 bp, in these cases the gene name is listed but no genome coordinates are provided (e.g.: E. coli gene acrB has an ortholog in H. influenzae, HI0895, but this gene’s upstream intergenic region was < 20 bp). Supplementary Table 3 caption. Excel sheets of the sites and the q-values for each of the Crp binding site prediction experiments in Table 1 of the text. The first sheet lists the Crp binding sites identified in the database of 2379 E. coli intergenic regions (described above) when using a product multinomial model (q-values in column E) and when combining evidence from the additional, independent species (q-values in column F); in this database, the number of sites evaluated for the Crp model was 390,054. The second sheet lists the Crp binding sites identified in the database of “reduced” E. coli intergenic regions (described above) when using a product multinomial model (q-values in column E) and when combining evide

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