| Parameter | Value |
|---|---|
| Analysis title | 72934_peaks analysis from Cistrome-GO |
| Mode | Solo mode |
| Species | hg38 |
| Peak bed file name | 72934_peaks.bed |
| Top peaks to use | 10000 |
| Peak number within the distance of 15*decay | 8127 |
| Half-decay distance | 10.0kb |
| 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 |
|---|
| GO terms | N, B, n, b | Enrichment | P-value | FDR | Genes |
|---|
| GO terms | N, B, n, b | Enrichment | P-value | FDR | Genes |
|---|
| GO terms | 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.