Identifying Potential Regulatory Elements by Transcription Factor Binding Site Alignment Using Partial Order Graphs

Identification and functional characterization of regulatory elements in the human genome is a challenging task. A sequence feature commonly used to predict regulatory activity is the co-occurrence...

[1]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[2]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[3]  Debbie K Goode,et al.  BMC Developmental Biology BioMed Central Database , 2007 .

[4]  Ilya Ioshikhes,et al.  Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors , 2013, Nucleic acids research.

[6]  Christopher J. Lee,et al.  Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems , 2004, Bioinform..

[7]  Martha L. Bulyk,et al.  UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions , 2010, Nucleic Acids Res..

[8]  Wyeth W. Wasserman,et al.  Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm , 2003, ISMB.

[9]  Fabrizio Smeraldi,et al.  POKer: a Partial Order Kernel for Comparing Strings with Alternative Substrings , 2017, ESANN.

[10]  G. Elgar,et al.  A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes , 2015, PloS one.

[11]  A. Waskiewicz,et al.  The role of Zic transcription factors in regulating hindbrain retinoic acid signaling , 2013, BMC Developmental Biology.

[12]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[13]  K. Mikoshiba,et al.  The expression of the mouse Zic1, Zic2, and Zic3 gene suggests an essential role for Zic genes in body pattern formation. , 1997, Developmental biology.

[14]  William Stafford Noble,et al.  Searching for statistically significant regulatory modules , 2003, ECCB.

[15]  E. Ukkonen,et al.  Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity , 2006, Cell.

[16]  Massimo Vergassola,et al.  Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo , 2002, BMC Bioinformatics.

[17]  Wolfgang Driever,et al.  Gene expression pattern Cloning and expression of the TALE superclass homeobox Meis2 gene during zebrafish embryonic development , 2001 .

[18]  Alexis Vandenbon,et al.  A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription , 2012, BMC Genomics.

[19]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[20]  Martin C. Frith,et al.  Cluster-Buster: finding dense clusters of motifs in DNA sequences , 2003, Nucleic Acids Res..

[21]  G. Rubin,et al.  Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Michael L. Cleary,et al.  Trimeric Association of Hox and TALE Homeodomain Proteins Mediates Hoxb2 Hindbrain Enhancer Activity , 1999, Molecular and Cellular Biology.

[23]  David J. Arenillas,et al.  JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles , 2013, Nucleic Acids Res..