A statistical analysis of the TRANSFAC database

Bajic, 2003, Content analysis of the core promoter region of human genes, In Silico Biol., 4, 0011 Birnbaum, 2001, cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships, Genome Res., 11, 1567, 10.1101/gr.158301 Bulyk, 2003, Computational prediction of transcription-factor binding site locations, Genome Biol., 5, 201, 10.1186/gb-2003-5-1-201 Cavener, 1987, Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates, Nucleic Acids Res., 15, 1353, 10.1093/nar/15.4.1353 Feingold, 2004, The ENCODE (ENCyclopedia of DNA Elements) project, Science, 306, 636, 10.1126/science.1105136 Fogel, 2004, Discovery of sequence motifs related to coexpression of genes using evolutionary computation, Nucleic Acids Res., 32, 3826, 10.1093/nar/gkh713 Heinemeyer, 1998, Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL, Nucleic Acids Res., 26, 362, 10.1093/nar/26.1.362 Kel, 2003, MATCH: a tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res., 31, 3576, 10.1093/nar/gkg585 Kellis, 2003, Sequencing and comparison of yeast species to identify genes and regulatory elements, Nature, 15, 241, 10.1038/nature01644 Kel-Margoulis, 2000, COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation, Nucleic Acids Res., 28, 311, 10.1093/nar/28.1.311 Kel-Margoulis, 2002, TRANSCompel: a database on composite regulatory elements in eukaryotic genes, Nucleic Acids Res., 30, 332, 10.1093/nar/30.1.332 Marino-Ramirez, 2004, Statistical analysis of over-represented words in human promoter sequences, Nucleic Acids Res., 32, 949, 10.1093/nar/gkh246 Matys, 2003, TRANSFAC®: transcriptional regulation, from pattern to profiles, Nucleic Acids Res., 31, 374, 10.1093/nar/gkg108 Moses, 2003, Position specific variation in the rate of evolution in transcription factor binding sites, BMC Evol. Biol., 3, 19, 10.1186/1471-2148-3-19 Mrowka, 2003, An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example, Am. J. Physiol. Regul. Integr. Comp. Physiol., 284, 1147, 10.1152/ajpregu.00448.2002 Qiu, 2002, Computational analysis of composite regulatory elements, Mamm. Genome, 13, 327, 10.1007/s00335-001-2141-8 Quandt, 1995, MatInd and MatInspector—new fast and versatile tools for detection of consensus matches in nucleotide sequence data, Nucleic Acids Res., 23, 4878, 10.1093/nar/23.23.4878 Sinha, 2003, YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation, Nucleic Acids Res., 31, 3586, 10.1093/nar/gkg618 Werner, 2003, The state of the art of mammalian promoter recognition, Brief. Bioinform., 4, 22, 10.1093/bib/4.1.22 Wingender, 1996, TRANSFAC: a database on transcription factors and their DNA binding sites, Nucleic Acids Res., 24, 238, 10.1093/nar/24.1.238 Wingender, 1997, TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation, Nucleic Acids Res., 25, 265, 10.1093/nar/25.1.265 Wingender, 2000, TRANSFAC®: an integrated system for gene expression regulation, Nucleic Acids Res., 28, 316, 10.1093/nar/28.1.316 Wingender, 2001, The TRANSFAC system on gene expression regulation, Nucleic Acids Res., 29, 281, 10.1093/nar/29.1.281 Wootten, 1996, Analysis of compositionally biased regions in sequence databases, Methods Enzymol., 266, 554, 10.1016/S0076-6879(96)66035-2