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)
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:
- Find the motifs associated with these peaks using Elementolab/ChIPseeqerFIRE.
- Perform a conservation analysis on these peaks. This is explained in Elementolab/ChIPseeqerCons
