Description
This track shows microRNA target sites in 3' UTRs as predicted by PicTar, based
on the RefSeq annotation of 3' UTRs.
Methods
The original PicTar algorithm was published in Krek et al.,
2005. The annotations displayed in this track are updated predictions as
published in Lall et al., 2006.
PicTar is a hidden Markov model
that assigns probabilities to 3' UTR subsequences as a binding site for a
microRNA, considers all possible ways the 3' UTR could be bound by microRNAs,
and then uses a maximum likelihood method to compute the optimal likelihood
under which the 3' UTR could be explained by microRNAs and background.
The score is this likelihood divided by background, i.e., the local
base composition of each 3' UTR is taken into account. To fit the
track conventions of the UCSC browser (integers), all scores were scaled by
the maximum score of all microRNA 3'-UTR scores observed. Note that the PicTar
algorithm
scores any 3' UTR that has at least one aligned conserved predicted binding
site for a microRNA, but then incorporates all possible binding sites into
the score, even if they appear to be non-conserved. Because the score for
a 3' UTR is a "phylo" average over all orthologous 3' UTRs used,
"scattered"
sites that appear in many species may boost the score, and individual sites
shown in the display may not be aligned and conserved in all species under
consideration.
Two levels of conservation can be chosen:
-- conservation among four vertebrates: human, mouse, rat, and dog
-- conservation among five vertebrates: human, mouse, rat, dog, and chicken
The latter settings have improved quality, but lower sensitivity.
For a detailed analysis of signal-to-noise ratios and sensitivity,
please refer to Lall et al., 2006.
Credits
Thanks to the Dominic Grün, Yi-Lu Wang, and Nikolaus Rajewsky for providing
this annotation. More detailed information about individual
predictions, including links to other databases, can be found on the
PicTar website,
a project of the
Rajewsky lab while at the New York University
Center for Comparative Functional Genomics.
References
Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P,
da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N.
Combinatorial microRNA target predictions.
Nat Genet. 2005 May;37(5):495-500.
Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N,
Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N.
A genome-wide map of conserved microRNA targets in C.
elegans.
Curr Biol. 2006 Mar 7;16(5):460-71.
|
|