Pvalue in annotated peak files

Question

[atsalaki]

Iam new to the field. I have annotated a chip-seq data bed peak file from ENCODE by taking the nearest to TSS genes in 5000 distance. From 50.000 records of the bed file i finaly found 1.500 records, genes that are upstream of the genes near TSS. These records have pvalues and qvalues. I wonder is it safe to take only the genes from the annotated peak file that have pvalue<0.05 or qvalue<0.05(cut-off )?i need the binding sites to cross correlate them with expression data on a vizualization tool forGene Regulatory Networks to determine if the ChIPed protein is involved in particular biological processes.I really dont know what to do.