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Back to Elementolab/ChIPseeqer_Tutorial


This analysis allows you to perform Pathway Analysis for the genes that have been associated with the detected ChIPseq peaks.

To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR, $CHIPSEEQERDIR/SCRIPTS and $PAGEDIR to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.

1. The first step is to make the required PAGE input files, using the ChIPseeqer output file (e.g., TF_targets.txt) as input.

To do this, type the following command:

ChIPseeqeriPAGE --peakfile=TF_targets.txt--suffix=TF_targets_iPAGE_data --runit=1

The following options are available:

--peakfile=FILE     file containing genomic regions
--lenuP=INT	    upstream length of the TSS. Default is 2000bp
--lendP=INT	    downstream length of the TSS. Default is 2000bp
--lenuDW=INT	    upstream length of the TES. Default is 2000bp
--lendDW=INT	    downstream length of the TES. Default is 2000bp
--suffix=STR        suffix for output files
--geneparts=STR     P, I, E, I1, I2 etc. Or you can use a combination of these separated by comma, eg. P,I
--genome=STR        can be hg18 (human),
                    mm9 (mouse),
                    dm3 (drosophila), or
                    sacser (for Saccharomyces cerevisiae)
--db=STR            can be refSeq (available for hg18, mm9, dm3), 
                    AceView (for hg18, mm9), 
                    Ensembl (for hg18, mm9, dm3)
                    UCSCGenes (for hg18, mm9). 
                    Default is refSeq.
--runit=INT         run PAGE directly if set to 1 (default = 1); if set to 1, no need to run PAGE manually

2. The second step is to run iPAGE (only if before you used --runit=0).

IMPORTANT: To download and install iPAGE see http://icb.med.cornell.edu/wiki/index.php/Elementolab/

If you have iPAGE installed on your computer, type the following command to run iPAGE:

page.pl --expfile=TF_targets_iPAGE_data.ORF --pathways=human_go_orf

The following options are available:

--expfile=FILE      expression/profile file (file format has two columns: gene names and expression measures (examples: continuous,  discrete)
--pathways=STR      species+annotation, options:human_go_orf, biocarta, kegg, HPRD_interactions, staudt_genesets
--exptype=STR       describes whether the expression profile is discrete or continuous
--cattypes=STR      specifies which part of the GO to use (F = molecular function, C = cellular component, P = biological process)
--minr=FLOAT        specifies how independent the categories should be, 0 by default meaning all informative pathways will be reported
--pathwaylist=FILE  use to restrict the number of evaluated pathways to a list (1 line per pathway) 
--ebins=INT         change the number of bins for continuous expression values (set to #genes/100 (100 genes per bin))
--randomize=INT     estimate the number of false positive pathways in your list INT = how many random runs to execute (do 3 minimum) 
--suffix=STR        to change the name of your output file when you run PAGE for different annotation categories (--suffix=KEGG)

The -- expfile option must be the .ORF file that has been created by ChIPseeqeriPAGE.

Example of PAGE output
Example of PAGE output

3. What can I do next ?

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