Supplementary material for "Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation"



This page contains data, softwares and supplementary results for the article "Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation", published in December 2005 in PLoS Computational Biology.


Full text is available at http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010069

Authors of the paper are Chang S Chan, Olivier Elemento and Saeed Tavazoie. CSC and OE have equally contributed to this work.
Contact: cschan AT princeton.edu, elemento AT princeton.edu, tavazoie AT genomics.princeton.edu


UPDATE JUNE 12TH, 2007: the C. elegans predictions for 5' and 3'UTR motifs, along with FIRE-predicted motifs, are now browsable via our new interface


Sequence data

- worm 3'UTRs (C. elegans, C. briggsae)
- fly 3'UTRs (D. melanogaster, D. pseudoobscura)


Softwares

- fastcompare source code (fastcompare_3UTR.c, cc -o fastcompare_3UTR fastcompare_3UTR.c -lm -O3 to compile)


Supplementary results

WORMS (C. elegans vs C. briggsae)

- conservation scores for all k-mers (7-mers, 8-mers, 9-mers), 442 highly conserved k-mers analyzed in the paper
- conserved sets for the 442 k-mers / aligned conserved sets (see note below for explanations)
- tool for highlighting highly conserved aligned k-mers on C. elegans / C. briggsae 3'UTRs  
- functional enrichments for the 442 k-mers
- k-mers complementary to the 5' extremity of miRNAs
- predicted miRNA targets, predicted aligned miRNA targets, targets with additional 3' complementarity to miRNAs
- gapped k-mers
- pairs of co-conserved k-mers
- known and novel miRNAs, detected by our miRNA discovery approach


FLIES (D. melanogaster vs D. pseudoobscura)

- conservation scores for all k-mers (7-mers, 8-mers, 9-mers), 497 highly conserved k-mers analyzed in the paper
- conserved sets for the 497 k-mers / aligned conserved sets (see note below for explanations)
- functional enrichments for the 497 k-mers
- k-mers complementary to the 5' extremity of miRNAs
- predicted miRNA targets, predicted aligned miRNA targets, targets with additional 3' complementarity to miRNAs
- gapped k-mers
- pairs of co-conserved k-mers
- known and novel miRNAs, detected by our miRNA discovery approach

note: the conserved set of a given k-mer corresponds to the genes that have the k-mer in both species (in their 3'UTR). The k-mers do not have to be aligned. On the other hand, the aligned conserved set is the subset of these genes where the k-mer is aligned (in ClustalW alignments of 3'UTRs).