29mammals: Difference between revisions
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==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/e/ed/29mammalsNovelExons_track.txt Novel Exons]== | |||
Summary: A list of identified novel conserved exons. | Summary: A list of identified novel conserved exons. | ||
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[http://genome.cshlp.org/content/17/12/1823.abstract Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes] | [http://genome.cshlp.org/content/17/12/1823.abstract Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes] | ||
Genome Res 17, 1823-1836, doi:gr.6679507 [pii] 10.1101/gr.6679507 (2007). | Genome Res 17, 1823-1836, doi:gr.6679507 [pii] 10.1101/gr.6679507 (2007). | ||
==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/a/a7/29mammals2xARs_track.txt human and primate] accelerated regions== | |||
Summary: Lists of human accelerated regions (HARs) and primate accelerated regions (PARs). | Summary: Lists of human accelerated regions (HARs) and primate accelerated regions (PARs). | ||
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Data provided by Katherine Pollard at ucsf.edu | Data provided by Katherine Pollard at ucsf.edu | ||
==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/5/5e/29mammalsExaptedElements_track.txt exaptations] of mobile elements== | |||
Summary: List of exapted elements identified as described in the reference mentioned below. | Summary: List of exapted elements identified as described in the reference mentioned below. | ||
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exaptations of mobile elements for likely regulatory functions | exaptations of mobile elements for likely regulatory functions | ||
in the human genome. In preparation (2011). | in the human genome. In preparation (2011). | ||
==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/f/fd/29mammalsMotifInstances_track.txt identified regulatory] motifs== | |||
Summary: A list of instances of identified regulatory motifs. | Summary: A list of instances of identified regulatory motifs. | ||
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[http://genome.cshlp.org/content/17/12/1823.abstract Reliable prediction of regulator targets using 12 Drosophila genomes] | [http://genome.cshlp.org/content/17/12/1823.abstract Reliable prediction of regulator targets using 12 Drosophila genomes] | ||
Genome Res 17, 1919-1931, doi:gr.7090407 [pii] 10.1101/gr.7090407 (2007). | Genome Res 17, 1919-1931, doi:gr.7090407 [pii] 10.1101/gr.7090407 (2007). | ||
==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/a/ac/29mammalsConstraintStructure_track.txt constraint structure] in promoters== | |||
Summary: A list of local maxima identified from the smoothed pi-scores in the core promoters of genes. | Summary: A list of local maxima identified from the smoothed pi-scores in the core promoters of genes. | ||
Data provided by Evan Mauceli at broadinstitute.org | Data provided by Evan Mauceli at broadinstitute.org | ||
==[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/2/28/29mammalsConstrainedElements_track.txt constrained elements]== | |||
Summary: Lists of constrained elements.<BR> | |||
For each 12-mer in the human genome a measure of constraint was | |||
scored using SiPhy (see reference below), both as a rate-based | |||
score (omega), and a measure that includes biased substitution | |||
patterns (pi). Those falling in annotated Ancestral Repeats | |||
were used as a background. An empirical cutoff score was set | |||
corresponding to 10% FDR, and all 12-mers above this score were | |||
considered significant. Overlapping significant 12-mers were | |||
clustered to yield larger elements. | |||
There are four tracks in this set: | |||
Constraint Elements pi lods score, data: mean: 7.214417, min: 1.711200, max: 16.237301, std: 1.364699 | |||
Constraint Elements pi branch length score, data: mean: 4.173642, min: -0.049714, max: 7.351400, std: 0.755658 | |||
Constraint Elements omega lods score, data: mean: 7.667489, min: 1.676100, max: 16.680599, std: 1.378213 | |||
Constraint Elements omega branch length score, data: mean: 4.255876, min: 0.301830, max: 7.376400, std: 0.731477 | |||
Data provided by Or Zuk at broad.mit.edu and Manuel Garber at broadinstitute.org | |||
Garber, M. et al. [http://bioinformatics.oxfordjournals.org/content/25/12/i54.short Identifying novel constrained elements by exploiting biased substitution patterns] | |||
Bioinformatics 25, i54-62, doi:btp190 [pii] 10.1093/bioinformatics/btp190 (2009) |
Revision as of 21:33, 22 March 2011
29 Mammal Paper supplemental materials
All tracks can be loaded into the hg18 genome browser: 29mammals custom tracks or the individual tracks can be loaded separately in the list below:
Novel Exons
Summary: A list of identified novel conserved exons.
Exons were identified using a version of CONGO (previously developed for the Drosophila genomes, see reference below) enhanced to handle mammalian exon prediction. The enhancements include a semi-Markov feature to model the short length distribution of mammalian exons, a synteny feature for recognizing duplicated regions, and an alternative training function to improve accuracy when performing an unbalanced prediction task (only ~1.5% of the human genome is protein-coding)
Data provided by Mike Lin at mit.edu
Lin, M. F. et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes Genome Res 17, 1823-1836, doi:gr.6679507 [pii] 10.1101/gr.6679507 (2007).
human and primate accelerated regions
Summary: Lists of human accelerated regions (HARs) and primate accelerated regions (PARs).
Regions with accelerated substitution rates in either lineage were identified by first defining candidate elements using the phastCons program (not including the lineage of interest) and then scoring those elements for accelerated substitution rates in the subtree (human or primate) of interest.
Data provided by Katherine Pollard at ucsf.edu
exaptations of mobile elements
Summary: List of exapted elements identified as described in the reference mentioned below.
Data provided by Craig Lowe at stanford.edu
Lowe, C. B. & Haussler, D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. In preparation (2011).
identified regulatory motifs
Summary: A list of instances of identified regulatory motifs.
A motif catalog was built from TRANSFAC, Jaspar, and Protein Binding Microarrays using a method similar to that described in the reference below, with extensions for position frequency matricies. Motif instances were identified genome-wide using a FDR of 60%.
Data provided by Pouya Kheradpour at mit.edu
Kheradpour, P., Stark, A., Roy, S. & Kellis, M. Reliable prediction of regulator targets using 12 Drosophila genomes Genome Res 17, 1919-1931, doi:gr.7090407 [pii] 10.1101/gr.7090407 (2007).
constraint structure in promoters
Summary: A list of local maxima identified from the smoothed pi-scores in the core promoters of genes.
Data provided by Evan Mauceli at broadinstitute.org
constrained elements
Summary: Lists of constrained elements.
For each 12-mer in the human genome a measure of constraint was scored using SiPhy (see reference below), both as a rate-based score (omega), and a measure that includes biased substitution patterns (pi). Those falling in annotated Ancestral Repeats were used as a background. An empirical cutoff score was set corresponding to 10% FDR, and all 12-mers above this score were considered significant. Overlapping significant 12-mers were clustered to yield larger elements.
There are four tracks in this set: Constraint Elements pi lods score, data: mean: 7.214417, min: 1.711200, max: 16.237301, std: 1.364699 Constraint Elements pi branch length score, data: mean: 4.173642, min: -0.049714, max: 7.351400, std: 0.755658 Constraint Elements omega lods score, data: mean: 7.667489, min: 1.676100, max: 16.680599, std: 1.378213 Constraint Elements omega branch length score, data: mean: 4.255876, min: 0.301830, max: 7.376400, std: 0.731477
Data provided by Or Zuk at broad.mit.edu and Manuel Garber at broadinstitute.org
Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns Bioinformatics 25, i54-62, doi:btp190 [pii] 10.1093/bioinformatics/btp190 (2009)