Elementolab/Find peaks and genes in pathway

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Find peaks and genes in pathway

This analysis can be followed after running Elementolab/ChIPseeqeriPAGE and allows you to find the peaks and genes that belong to a specific pathway assigned by PAGE.

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

1. Type the command:

 Find_peaks_and_genes_in_pathway.pl --expfile=TF_targets.txt.ORF --overlapfile=TF_targets.txt.NM_peaks --bin=1 --pathway=GO:0045892 \
--species=human_go_orf --prefix=output
-expfile=FILE	   The text file given as input in PAGE.
-overlapfile=FILE  (Optional) The NM_peaks file created by ChIPseeqeriPAGE (You need this to extract the peaks. 
                   You can skip it if you only want to extract the genes)
-bin=INT	   Indicates the categories of genes in PAGE. 0 stands for the background genes, and 1 for the input genes. 
                   If more input gene categories were used then bin=2 and so on should be used.
-pathway=STR       Which pathway to look for. For example, GO:0042436 or hsa12345. If not set, looks for all pathways found.
-species=STR       Can be human_go_orf, biocarta, kegg, HPRD_interactions, staudt_genesets (mouse_go_orf for mouse)
-prefix=STR        The prefix of the output file(s)
Example of PAGE output
Enlarge
Example of PAGE output

2. See the results.

The output of the script are: a peaks.pathway.txt and a genes.pathway.txt file.

The .genes.pathway.txt file looks like this:

PEX14	NM_004565	peroxisomal biogenesis factor 14	1
ZNF238	NM_205768/NM_006352	zinc finger protein 238 isoform 1/zinc finger protein 238 isoform 2	1
SMARCE1	NM_003079	SWI/SNF-related matrix-associated	1
BCL6	NM_001130845/NM_001706/NM_001134738	B-cell lymphoma 6 protein isoform 1/B-cell lymphoma 6 protein isoform 2	1

the .peaks.pathway.txt file looks like this:

chr1	10457360	10457535	PEX14	NM_004565	peroxisomal biogenesis factor 14	1
chr1	242280371	242280670	ZNF238	NM_205768/NM_006352	zinc finger protein 238 isoform 1/zinc finger protein 238 isoform 2	1
chr17	36057651	36057809	SMARCE1	NM_003079	SWI/SNF-related matrix-associated	1

3. What can I do next ?

Once you get a list of peaks saved in a text file, you can:

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