Supplementary web site for "A universal framework for regulatory element discovery across all genomes and data-types"
Olivier Elemento*, Noam Slonim* and Saeed Tavazoie (* OE and NS contributed equally)
To contact us: {elemento, nslonim, tavazoie}@princeton.edu
Click here to access the paper at the Molecular Cell Web site.
How can I use FIRE ?
FIRE can be downloaded and installed on a Unix (or Cygwin) machine. Click here to download FIRE. Here is a release log and recently fixed bugs.
FIRE comes with pre-packaged sequence data for many well-studied organisms. You can download data for:
yeast (S. cerevisiae; FIRE name: yeast),
fission yeast (S. pombe; FIRE name: pombe),
yeast (S. bayanus; FIRE name: bayanus) (made by Konrad Karczewski, Princeton),
C. albicans (FIRE name: calbicans),
P. falciparum (FIRE name: malaria),
worm (C. elegans; FIRE name: worm),
drosophila (D. melanogaster; FIRE name: drosophila),
arabidopsis (A. thaliana; FIRE name: arabidopsis),
poplar (P. trichocarpa; FIRE name: poplar),
rice (O. sativa; FIRE name: rice),
sea squirt (C. intestinalis; FIRE name: ciona),
human (H. sapiens; FIRE name: human),
mouse (M. musculus; FIRE name: mouse),
rat (R. norvegicus; FIRE name: rat) (kindly donated by Bernd Jagla, Columbia),
chicken (G. gallus; FIRE name: chicken),
ecoli_tu (E. coli transcription units; FIRE name: ecoli_tu) (made by Hani Goodarzi, Princeton)
If your favorite organism is not in the list and you would like us to add it, please contact us. You can also analyze your own sequences using the command line program (see tutorial or contact us for more details).
FIRE is a powerful program, with many options and many output files. Click here for a tutorial on how to install and use FIRE.
FIRE can also be used online. Click here for the online FIRE application (created by Bambi Tsui, Princeton).
Supplementary results
Yeast (S. cerevisiae)
Clustered stress microarray dataset (Gasch et al, 2000):
full results when using 6-mers
Array-by-array analysis of the stress microarray dataset :
combined array-by-array heatmap
P. falciparum
Phase analysis of the intra-erythrocytic developmental cycle (IDC, from Bozdech, Llinas et al, 2003):
phase profile for ~2,700 genes
Array-by-array analysis of the IDC (not restricted to periodically expressed genes):
combined array-by-array heatmap
Worm
Clustered C. elegans compendium from Stuart Kim's lab (Kim et al, 2001, Science):
Array-by-array analysis of the C. elegans compendium :
Drosophila
Spatio-temporal expression patterns assessed using in situ hybridization (Tomancak et al, 2002):
all results for all 55 patterns
Early embryonic enhancers
124 enhancer sequences (link to D. Papatsenko's web site)
FIRE motifs for Bicoid and Dorsal enhancers