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, elemento, tavazoie}@princeton.edu
Click here to access the paper at the Molecular Cell Web site.
Click here to access supplemental data and supplemental results..
How can I use iPAGE?
iPAGE can be downloaded and installed on a Unix (or Cygwin) machine. Click here to download iPAGE.
It can also be accessed through a web interface (created by Bambi Tsui, Princeton). Click here to access iPAGE.
A GUI for iPAGE is available for MS Windows and MAC OS X users. The installation information and a tutorial on how to use the interface is available here.
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 intearction map (.pdf)
Pathway-regulatory intearction 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 here 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' elemenes (.txt)
Cancer Pathway Regulatory Map for 3' elemenes (.txt)
Experimental validations
Decoy vs. scrambled oligos: AAAA[AGT]TT
Expression profile of decoy-transfected vs. scrambles 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.