|Analysis title||72934_peaks analysis from Cistrome-GO|
|Peak bed file name||72934_peaks.bed|
|Top peaks to use||10000|
|Peak number within the distance of 15*decay||8127|
|FDR cutoff of GO/KEGG terms to return||0.2|
|Minimum and maximum gene number in GO and KEGG gene sets||10,2000|
8.941% of peaks are located in the promotor region. This is less than the 20% promoter-type threshold so the the decay distance is set to 10.0kb, appropriate for enhancer-type analysis. The decay distance can be specified in the options.
|Gene||Coordinate||Visualize||Peak number||RP score||adjusted RP score||Ranked by adjust RP score|
|KEGG pathways||N, B, n, b||Enrichment||P-value||FDR||Genes|
First, we separate genes in the differential expression list into up-regulated genes and down-regulated genes using logFoldChange. Then using user customized FDR and logFoldChange cutoff (FDR <= 0.05 absolute logFoldChange >= 1.0 by default) to get significantly differentially expressed genes which are regarded as the true positive. We use the RP score to predict whether a gene is significantly differentially expressed. Thus, we can draw the receiver operating characteristic (ROC) curve and precision-recall (RP) curve and calculate AUC respectively. Those information can help users to judge the (activating, repressive, and both) regulation direction of the transcription factor.