Following a request from somebody at Virginia Tech, we have added Rice to the list of organisms supported by FIRE. We used the following gene identifiers:
LOC_Os11g37320
LOC_Os01g12410
LOC_Os01g25110
LOC_Os02g07360
LOC_Os11g45360
etc.
To analyze Rice expression data, you’ll need to download FIRE, then download the rice_data.zip file. The download site is http://tavazoielab.princeton.edu/FIRE/
This is the title of our latest paper in Blood, which is also my first one at Weill Cornell and my first one as (joint) corresponding author.
http://bloodjournal.hematologylibrary.org/cgi/content/abstract/blood-2008-12-193037v1
My lab doesn’t work on plants, but following a request from somebody in Malcom Campbell’s lab at U of Toronto, I’ve just added the Poplar to the list of organisms supported by FIRE.
The genome data comes from http://genome.jgi-psf.org/Poptr1_1/
To analyze Poplar expression data, you’ll need to download FIRE, then download the poplar_data.zip file from http://tavazoielab.princeton.edu/FIRE/
I tested it on a clustered dataset of Poplar tissue expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6422), and I got very impressive results. The test expression profile is included in the EXPFILES directory in poplar_data.zip file.
Pat Brown (the inventor of microarrays) just published a paper in PLoS Biology in which he described the identification of mRNA targets for 40 RNA-binding proteins. Not only it’s a very interesting study that emphasizes the extent of post-transcriptional regulation, but they also extensively use FIRE for motif discovery ( along with their homebrewed approach)
The other paper in Nature by Ruschlow and colleagues describes a protein that binds to a putative reglatory element (CAGGTAG) that we identified in our collaboration with Eric Wieschaus as highly over-represented upstream of the earliest zygotic genes in the Drosophila embryo (De Renzis, Elemento et al, PLoS Biology, 2007).They used one-hybrid assay to identify the zinc finger protein called Zelda.
The article is nicely titled “Decoding the regulatory genome”.
Molecular Cell table of content (Oct 26th issue):
http://www.molecule.org/content/current
Direct link to the paper:
http://www.molecule.org/content/article/fulltext?uid=PIIS1097276507006661
FIRE web site (to access the Web interface or download the software) :
http://tavazoielab.princeton.edu/FIRE/
The first two (mostly experimental) papers that used and cite FIRE have also been submitted this week, one to PNAS, the other to Nature Genetics.
Update Oct 29th: Nature Reviews Genetics is going to publish a “Research Highlight” on our paper.
Update Nov 8th: The paper was rated as ‘Must Read’ by the Faculty of 1000 Biology (F1000 factor 6.0)
Update Nov 10th: FIRE is also available for commercial licensing through Princeton University (totally free for academia of course).
If you are attending the Molecular Parasitology meeting at Woods Hole this year, make sure you hear the talk by Erandi in Manuel Llinas’ lab at Princeton. Using protein binding microarrays (PBM), Manuel, his group and his Harvard collaborators have validated 3 of the Plasmodium falciparum motifs we predicted using FIRE in our forthcoming Molecular Cell paper. Their excellent work also happens to be the first characterization of specific DNA-binding proteins in Plasmodium.
The FIRE paper has recently been accepted to Molecular Cell. The tentative publication date is Oct 26, 2007. We are going to make the software available soon (we need a couple more weeks to clean up the code, finish writing the tutorial, and take care of intellectual property questions).
I just submitted an abstract for the CSHL Systems Biology 2007 meeting (March 29 to April 1, 2007). You can find the abstract here.
Update : here is the poster we presented.
