iPAGE
Supplementary web site for “Revealing global regulatory perturbations across human cancers”
Hani Goodarzi*, Olivier Elemento* and Saeed Tavazoie (* HG and OE contributed equally)
To contact us: {goodarzi@princeton.edu, ole2001@med.cornell.edu, st2744@columbia.edu}
Molecular Cell. 2009 Dec 11; 36:900-911 PDF.
Click here to access supplemental data and supplemental results.
How can I use iPAGE?
IGET: Use iPAGE online
iPAGE is the pathway discovery component of IGET, an integrated platform for exploring large-scale gene expression and protein behavior dynamics. Use IGET to discover motifs, pathways, and interactions.
iPAGE can be downloaded and used as a command line program (on a Unix or Cygwin machine), via a graphical user interface (on a Microsoft Windows or Apple Mac machine), or as an online tool.
iPAGE comes with pre-packaged sequence data for many well-studied organisms.
If your favorite organism is not in the list and you would like us to add it, please contact us. You can also add your own organisms (see tutorial or contact us for more details).
iPAGE is a powerful package which in conjunction with FIRE provides a complete meta-analysis of whole-genome datasets. Click here for a tutorial on how to install and use iPAGE. If you want to use "pathway-regulatory map generator" (which is part of iPAGE) you need to install FIRE as well.
Supplemental results
Discovering deregulated pathways in bladder carcinoma
Data from Dyrskjot L, et al. (2004) Cancer Res 64, 4040-4048.
input data (continuous: s.(1-p))
iPAGE results (.pdf)
iPAGE results (.txt)
FIRE results (.pdf)
FIRE results (.txt)
Pathway-regulatory interaction map (.pdf)
Pathway-regulatory interaction map (.txt)
Comparative analysis of Bukitt's lymphoma vs. diffuse large-B-cell lymphoma
Data from Hummel M, et al. (2006) N Engl J Med 354, 2419-2430.
input data (discrete: 110 clusters)
iPAGE results (.pdf)
iPAGE results (.txt)
FIRE results (summarized.pdf)
FIRE results (summarized.txt)
Pathway-regulatory interaction map (.pdf)
Pathway-regulatory interaction map (.txt)
FIRE results (complete.pdf)
FIRE results (complete.txt)
Global regulatory perturbations across human cancers
The input data has been gathered from a range of sources (see Table S2, Supplementary Materials for the complete list).
The input files can be found here.
Cancer Pathway Map (.pdf)
Cancer Pathway Map (.txt)
Cancer Regulatory Map (.pdf)
Cancer Regulatory Map (.txt)
Cancer Pathway Regulatory Map (.pdf)
Cancer Pathway Regulatory Map for 5' elements (.txt)
Cancer Pathway Regulatory Map for 3' elements (.txt)
Experimental validations
Decoy vs. scrambled oligos: AAAA[AGT]TT
Expression profile of decoy-transfected vs. scrambled transfected MDA-MB-231 cells.
FIRE results (non-discovery mode) (.pdf)
iPAGE results (.pdf)
FIRE results (.pdf)
Elk1 transcription factor knock-down
Expression profile of Elk1 siRNA transfected vs mock-transfected MDA-MB-231 cells.
iPAGE results (.pdf)
FIRE results (.pdf)
NF-Y (NFYA) transcription factor knock-down
Expression profile of NFYA siRNA transfected vs mock-transfected MDA-MB-231 cells.
iPAGE results (.pdf)
FIRE results (.pdf)