Installing and using iPAGE: a basic tutorial

Installation

Download the code (e.g, iPAGEvx.x.zip) to your machine. If you want, you can use wget to get the code:

wget https://tavazoielab.c2b2.columbia.edu/iPAGE/iPAGEvx.x.zip

Unzip the .zip file using unzip (files will be unzipped in a iPAGEvx.x/ directory)

unzip iPAGEvx.x.zip

Then, go to iPAGEvx.x/ and run make:

cd iPAGEvx.x
make

Finding informative pathways

The current implementation of iPAGE is meant to be executed from the same directory where all the scripts reside (in the iPAGEvx.x/ directory if you've followed the instructions above). If you want to run iPAGE from another directory, you should define PAGEDIR variable:

export PAGEDIR=/path/to/iPAGE/

If you don't set the PAGEDIR variable, iPAGE assumes the current path as the iPAGE home directory.

The basic command line syntax for iPAGE is :

perl page.pl --expfile=<inp> --species=<spp> --exptype=<typep>

where <inpp> indicates the input expression profile, <spp> indicates the species, and <typep> indicates whether the expression profile is discrete (e.g., cluster indices) or continuous (e.g., expression values obtained from a single microarray experiment).

For example, the following command line will run a test for an arbitrary continuous dataset :

perl page.pl --expfile=./TEST/bladder.exp --species=human --exptype=continuous --ebins=15

iPAGE creates an expfile_PAGE where the results are saved. The output files include:

expfile.summary.pdf(eps)	P-value heatmap combining significant categories (main figure)
pvmatrix.txt	Contains the data used to create the "expfile.summary.pdf" file
pvmatrix.txt.killed	Lists the categories that were significant but they were ommitted because of their redundancy

Finally, here are some useful parameters that can be set for page.pl script:

--goindexfile=FILE --gonamesfile=FILE	Uses these files to run iPAGE instead of using "--species=sp" (defining --species would over-write these two parameters)
--independence=1/0	If set to 1, removes the redundant categories; otherwise, all the significant catgeories are included (default=1)
--cattypes=F,P,C	For GO:terms you can change this parameter to "--cattypes=P,C" or any other combination
--datafile=FILE --draw_sample_heatmap=true	In the "expfile.summary.pdf" it draws a heatmap of the average expression for each of the clusters.

Buidling pathway motif interaction maps

The PRMG script (prmg.pl) is part of the iPAGE package and is located in the PAGEvx.x directory; however, it also relies on FIRE outputs to run (FIRE is available at https://tavazoielab.c2b2.columbia.edu/FIRE/):

export PAGEDIR=/path/to/iPAGE
perl prmg.pl --expfile=<inp> --species=<sp>

where <inp> indicates the input expression profile, <sp> indicates the species. The script does not work on expfile itself, but uses it to locate iPAGE and FIRE summary files (in expfile_PAGE and expfile_FIRE directories).

For example, the following command line will run PRMG on a continuous expression profile:

perl prmg.pl --expfile=./TEST/continuous.exp --species=human_go

The results are written to a motif_cat.cdt file and the graphical representations are created in the motif_cat.eps and motif_cat.pdf files.

For interactions with protein motifs (FIRE-pro results), prmg_protein.pl rather than prmg.pl should be used.