This track shows microRNA target sites in 3' UTRs as predicted by PicTar, based on the 3' UTRs annotated by WormBase and on UCSC's 3' UTRs predictions (see below).
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.
For the nematode target predictions, three species were used: C. elegans, C. briggsae and C. remanei. Because 3' UTRs are rarely annotated in WormBase or RefSeq, UCSC "guessed" the 3' UTR sequences for all transcripts without 3' UTRs annotations by extending the CDS 500 bases downstream of the stop codon, and stopping when another CDS was hit.
For a detailed analysis of signal-to-noise ratios and sensitivity, please refer to Lall et al., 2006.
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.
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.