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Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller* and Elia Stupka*

Genome Biology 2006, 7:R56 doi:10.1186/gb-2006-7-7-r56

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BioMed Central: 7 citations

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Conservation of core gene expression in vertebrate tissues

Esther T Chan, Gerald T Quon, Gordon Chua, Tomas Babak, Miles Trochesset, Ralph A Zirngibl, Jane Aubin, Michael JH Ratcliffe, Andrew Wilde, Michael Brudno, Quaid D Morris, Timothy R Hughes Journal of Biology 2009, 8:33 (16 April 2009)

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High conservation of tissue-specific expression is found across vertebrates yet there is a lack of conservation in common regulatory sequences/signatures.

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Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

David M McGaughey, Zachary E Stine, Jimmy L Huynh, Ryan M Vinton, Andrew S McCallion BMC Genomics 2009, 10:8 (7 January 2009)

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TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements

Alison P Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh BMC Genomics 2007, 8:441 (29 November 2007)

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CONDOR: a database resource of developmentally associated conserved non-coding elements

Adam Woolfe, Debbie K Goode, Julie Cooke, Heather Callaway, Sarah Smith, Phil Snell, Gayle K McEwen, Greg Elgar BMC Developmental Biology 2007, 7:100 (30 August 2007)

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Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction

Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Strähle, Ferenc Müller Genome Biology 2007, 8:R106 (8 June 2007)

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Investigation of the ar-C midline enhancer of sonic hedgehog orthologs and paralogs from distantly related vertebrate lineages identified lineage-specific motif changes; exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity.

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Multiple non-collinear TF-map alignments of promoter regions

Enrique Blanco, Roderic Guigó, Xavier Messeguer BMC Bioinformatics 2007, 8:138 (24 April 2007)

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Transcription factor binding site maps are a powerful way to reveal conserved regulatory elements within both promoters and 3' untranslated regions that may be missed by sequence alignments when sequence conservation is lacking.

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Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar Genome Biology 2007, 8:R15 (2 February 2007)

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Invertebrate conserved noncoding elements (CNEs) are associated with the same core set of genes as vertebrate CNEs, and may reflect the parallel evolution of enhancers in the gene regulatory networks that define alternative animal body plans.

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