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),
fission yeast (S. pombe),
yeast (S. bayanus) (made by Konrad Karczewski, Princeton),
C. albicans,
P. falciparum,
worm (C. elegans),
drosophila (D. melanogaster),
arabidopsis (A. thaliana),
sea squirt (C. intestinalis),
human (H. sapiens),
mouse (M. musculus),
rat (R. norvegicus) (kindly donated by Bernd Jagla, Columbia),
chicken (G. gallus),
ecoli_tu (E. coli transcription units) (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):

clustering partition

full results

full results when using 6-mers

Array-by-array analysis of the stress microarray dataset :

all results for all arrays

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

full results

Array-by-array analysis of the IDC (not restricted to periodically expressed genes):

all results for all arrays

combined array-by-array heatmap

Worm

Clustered C. elegans compendium from Stuart Kim's lab (Kim et al, 2001, Science):

clustering partition

full results

Array-by-array analysis of the C. elegans compendium :

all results for all arrays

Drosophila

Spatio-temporal expression patterns assessed using in situ hybridization (Tomancak et al, 2002):

all results for all 55 patterns

combined heatmap

Early embryonic enhancers

124 enhancer sequences (link to D. Papatsenko's web site)

FIRE motifs for Bicoid and Dorsal enhancers

Human

Clustered human tissue expression dataset (Su et al, 2004):

clustering partition

full results

Array-by-array analysis of the human tissue expression dataset :

all results for all arrays

Mouse

Clustered mouse tissue expression dataset (Su et al, 2004):

clustering partition

full results

Array-by-array analysis of the human tissue expression dataset :

all results for all arrays