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Methods: Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
- Mathieu Blanchette,
- Alain R. Bataille,
- Xiaoyu Chen,
- Christian Poitras,
- Josée Laganière,
- Céline Lefèbvre,
- Geneviève Deblois,
- Vincent Giguère,
- Vincent Ferretti,
- Dominique Bergeron,
- Benoit Coulombe,
- and François Robert
Genome Res. May 2006 16: 656-668; Published in Advance April 10, 2006, doi:10.1101/gr.4866006
...to each PWM using a log-likelihood ratio score with a third-order Markov background model parameterized based on the local GC content. Corresponding orthologous positions in mouse and rat s were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned...
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Chicken Special/Resources: Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates
- Wendy A. Kellner,
- Robert T. Sullivan,
- Brian H. Carlson,
- and James W. Thomas
Genome Res. January 2005 15: 166-173; Published in Advance December 8, 2004, doi:10.1101/gr.3066805
...with the orthologous sequence in other placental mammals. In the case of dog, cat, cow, and pig, we were able to confirm that this prediction was in fact valid &gt;75% of the time (see Methods). For the human–mouse–rat alignments, a more empirical scoring matrix and cutoff threshold were implemented (for details, see...
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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
...genes, the classic local alignment methods would yield n2 alignments between all pairs of these. Despite some of the disadvantages, local alignments were used for comparison of the human and mouse s (Ma et al. 2002; Schwartz et al. 2003) and for the human/mouse/rat three-way alignments (Blanchette et al...
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LETTER: Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- David C. King,
- James Taylor,
- Laura Elnitski,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. August 2005 15: 1051-1060; Published in Advance July 15, 2005, doi:10.1101/gr.3642605
...., and Chiaromonte, F. 2004 . Regulatory potential scores from -wide three-way alignments of human, mouse and rat. Genome Res. 14 : 700 –707. ↵ Lander, E.S., Linton, L.M., Birren, B., Nusbaum...
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Methods: ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
- James Taylor,
- Svitlana Tyekucheva,
- David C. King,
- Ross C. Hardison,
- Webb Miller,
- and Francesca Chiaromonte
Genome Res. December 2006 16: 1596-1604; Published in Advance October 19, 2006, doi:10.1101/gr.4537706
.... , Hardison, R.C. , Chiaromonte, F. ( 2004 ) Regulatory potential scores from -wide three-way alignments of human, mouse, and rat . Genome Res. 14 : 700 – 707 . ↵ Korf, I. , Flicek, P. , Duan, D. , Brent, M.R. ( 2001 ) Integrating genomic homology into gene structure prediction . Bioinformatics 17 : S...
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LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
..., such as exons and CRMs, align among human, mouse, and rat s ( Waterston et al. 2002 ; Gibbs et al. 2004 ), but many CRMs fail to align between human and chicken ( Hillier et al. 2004 ). Statistical methods that score multiple sequence alignments to find highly constrained elements are being developed...
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RESOURCE: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
- Eugene Berezikov,
- Victor Guryev,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. January 2004 14: 170-178; Published in Advance December 12, 2003, doi:10.1101/gr.1642804
...restricted ourselves to five vertebrate organisms for which assembled and annotated s are available in the Ensembl database ( Clamp et al. 2003 )as follows: human, rat, mouse, fugu, and zebrafish. We used data from TransFac database ( Matys et al. 2003 )to build a reference set of regulatory sites...
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Research: Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
- Emily S. Wong,
- David Thybert,
- Bianca M. Schmitt,
- Klara Stefflova,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. February 2015 25: 167-178; Published in Advance November 13, 2014, doi:10.1101/gr.177840.114
...-species variability compared to TFindependent genes across taxa and TFs (Kolmogorov-Smirnov one-tail test: HNF4A mean across species P = 0.67; CEBPA mean across species P = 3.63 10#1;2; FOXA1mean across species P = 0.35). We obtained similar results when we extended our analysis to include BL6 to rat evolutionary...
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LETTER: Dispensability of mammalian DNA
- Cory McLean and
- Gill Bejerano
Genome Res. November 2008 18: 1743-1751; Published in Advance October 2, 2008, doi:10.1101/gr.080184.108
..., alignment, and structural RNA migration artifacts (Supplemental Fig. S1). We use whole sequences of two rodents (mouse and rat), two primates (human and macaque), and a close carnivore outgroup species (dog). By examining sequences conserved between human, macaque, and dog, with no orthologous DNA in either...
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Research: Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder
- Przemyslaw Szafranski,
- Avinash V. Dharmadhikari,
- Erwin Brosens,
- Priyatansh Gurha,
- Katarzyna E. Kołodziejska,
- Ou Zhishuo,
- Piotr Dittwald,
- Tadeusz Majewski,
- K. Naga Mohan,
- Bo Chen,
- Richard E. Person,
- Dick Tibboel,
- Annelies de Klein,
- Jason Pinner,
- Maya Chopra,
- Girvan Malcolm,
- Gregory Peters,
- Susan Arbuckle,
- Sixto F. Guiang III,
- Virginia A. Hustead,
- Jose Jessurun,
- Russel Hirsch,
- David P. Witte,
- Isabelle Maystadt,
- Neil Sebire,
- Richard Fisher,
- Claire Langston,
- Partha Sen,
- and Paweł Stankiewicz
Genome Res. January 2013 23: 23-33; Published in Advance October 3, 2012, doi:10.1101/gr.141887.112
...sequences were assessed using the UCSC ‘‘Conservation’’ and ‘‘73 Reg potential’’ tracks, respectively. The 73 regulatory potential scores are computed from alignments of human, chimpanzee, macaque, mouse, rat, dog, and cow s using log-ratios of transition probabilities from two variable order Markov models...

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