29mammals

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:

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)

[ Base Level Measure of Constraint]

Summary: Base-level measure of constraint scored using SiPhy (see reference above), both as a rate-based score (omega) and a measure that includes biased substitution patterns (pi).

Data Not Available on UCSC Genome Browser.

Contact: Manuel Garber <mgarber@broadinstitute.org>

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).

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).

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).

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