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BMC Bioinformatics

Table 2 Pathways analysis between the ETS1 distal and promoter peaks.

		Distal Peaks	Promoter peaks
T/B cell related	Gene Ontology
	Leukocyte differentiation, GO:0002521	p < 0.001	p < 1
	Lymphocyte activation, GO:0046649	p < 0.001	p < 1
	Hemopoiesis, GO:0030097	p < 0.001	p < 1
	Hemopoietic or lymphoid organ development, GO:0048534	p < 0.001	p < 1
	Immune response, GO:0006955	p < 0.01	p < 1
	Immune system development, GO:0002520	p < 0.01	p < 1
	B cell proliferation, GO:0042100	p < 0.01	p < 1
	B cell activation, GO:0042113	p < 0.001	p < 1
Others	Biopolymer catabolic process, GO:0043285	p < 1	p < 1e-29
	RNA splicing, GO:0008380	p < 1	p < 1e-50
	DNA metabolic process, GO:0006259	p < 1	p < 1e-29
T/B cell related	SignatureDB
	Tcell_PIind_CalciumDefPtdown4x_Feske_Fig6	p < 1e-05	p < 1
	CD40_upregulated_Burkitt_lymphoma	p < 0.001	p < 1
	CD40_downregulated_Burkitt_lymphoma	p < 0.01	p < 1
	Pax5_repressed	p < 0.01	p < 1
	Tcell_PIind4x_Feske_Fig6	p < 1e-08	p < 1
	Tcell_PIind_CsAdown4x	p < 1e-04	p < 1
Others	Ribosomal_protein	p < 1	p < 1e-06
	Myeloma_PR_subgroup_up	p < 1	p < 1e-05

The table shows some of the pathways and lymphoma-related signatures that were found enriched in the distal peaks and the promoter peaks groups. The distal peaks group was highly associated with T cell and B cell related ontologies and signatures, while for the promoter peaks group more general and housekeeping categories were enriched. The Gene Ontology and the SignatureDB gene expression signatures were used for this analysis (ChIPseeqeriPAGE module). The p-values for each pathway for both groups are also shown.

ISSN: 1471-2105