29mammals

29 Mammal Paper supplemental materials

Custom tracks on hg18 genome browser:

1. 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).

2. 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 

3. 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).

4. 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).

5. 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