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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...-scale unstranded RNA-seq data could be valuable in three ways. For example, other public transcriptome databases, such as the TCGA Consortium (Ciriello et al. 2013; Kandoth et al. 2013), the GTEx Project (The GTEx Consortium 2013), the Human Protein Atlas (Uhlen et al. 2010, 2015), and NCBI GEO, include large...
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Methods: Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- Diana Kolbe,
- James Taylor,
- Laura Elnitski,
- Pallavi Eswara,
- Jia Li,
- Webb Miller,
- Ross Hardison,
- and Francesca Chiaromonte
Genome Res. April 2004 14: 700-707; doi:10.1101/gr.1976004
..., conserved noncoding segments are strong candidates for experimental verification (e.g., Hardison et al. 1997a ; Loots et al. 2000 ). On the other hand, sequence conservation by itself may not differentiate between regulatory segments and other functional regions, such as non-translated RNA genes. We...
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LETTER: Conserved Noncoding Sequences in the Grasses
- Dan Choffnes Inada,
- Ali Bashir,
- Chunghau Lee,
- Brian C. Thomas,
- Cynthia Ko,
- Stephen A. Goff,
- and Michael Freeling
Genome Res. September 2003 13: 2030-2041; doi:10.1101/gr.1280703
...Conserved Noncoding Sequences in the Grasses 4 Dan Choffnes Inada 1 , Ali Bashir 1 , Chunghau Lee 1 , Brian C. Thomas 2 , Cynthia Ko 3 , Stephen A. Goff 3 , and Michael Freeling 1 , 5 1 Department...
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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
...Heyningen 2005; Kleinjan and Coutinho 2009). To date, this phenomenon has been reported for more than 40 genetic loci in the human ; however, the underlying mechanism remains unknown. Of interest, a 7.4-kb cis-regulatory deletion disrupting conserved noncoding sequences and their interaction...
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Methods: MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
- Peter D. Keightley and
- Toby Johnson
Genome Res. March 2004 14: 442-450; doi:10.1101/gr.1571904
.... Inferences based on such alignments, such as estimates of the degree of sequence divergence or conservation, are therefore almost certainly biased ( Thorne et al. 1991 ). Such heuristic methods have frequently been used for alignment of noncoding DNA from diverse species (e.g., Gu and Li 1995 ; Jareborg et...
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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
.... These can include the presumptive start site for transcription ( Trinklein et al. 2003 ), matches to transcription factor binding sites ( Wingender et al. 2001 ; Sandelin et al. 2004a ), overrepresentation of motifs in coexpressed genes ( Spellman et al. 1998 ), and noncoding sequence conservation (for...
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LETTER: Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
- Bárbara Negre,
- Sònia Casillas,
- Magali Suzanne,
- Ernesto Sánchez-Herrero,
- Michael Akam,
- Michael Nefedov,
- Antonio Barbadilla,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. May 2005 15: 692-700; doi:10.1101/gr.3468605
.... ↵ Dubchak, I., Brudno, M., Loots, G.G., Pachter, L., Mayor, C., Rubin, E.M., and Frazer, K.A. 2000 . Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10 : 1304 –1306. ↵ Duncan, I. 1987 . The bithorax complex. Annu. Rev. Genet. 21 : 285 –319. ↵ Ewing, B...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
.../30 revealed a much sparser set of nearly parallel connections (Supplemental Fig. S2A). As expected, comparisons of three or more genomic sequences allowed clean results at lower thresholds than pairwise comparisons, improving the signal-to-noise ratio ( Fig. 2A,C ; Supplemental Fig. S2A,B). Three-way...
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LETTER: Close sequence comparisons are sufficient to identify human cis-regulatory elements
- Shyam Prabhakar,
- Francis Poulin,
- Malak Shoukry,
- Veena Afzal,
- Edward M. Rubin,
- Olivier Couronne,
- and Len A. Pennacchio
Genome Res. July 2006 16: 855-863; Published in Advance June 12, 2006, doi:10.1101/gr.4717506
...comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of evolutionarily close and distant sequence comparisons. To address this problem, we identified evolutionarily conserved noncoding regions...
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ARTICLE: Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences
- Casey M. Bergman and
- Martin Kreitman
Genome Res. August 1, 2001 11: 1335-1345; doi:10.1101/gr.178701
...of conserved noncoding DNA is sufficient for both intergenic and intronic compartments of the Drosophila . Methodological Considerations for the Interpretation of Noncoding Conservation Because there is no reading frame to constrain alignments, results based on pairwise sequence comparisons of noncoding DNA...

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