At the end of the enrichment analysis the results will be shown within a downloadable datatable and an interactive barplot.
The barpots shows the first 10 top ranking results ranked by combined-score. Moreover hovering on the bar, corrisponding to the TF of interest, you can retrieve information about the underlying TF- ChIP seq experiment.
In the datatable nine columns are present for each transcription factor:
- Target factor: antibody target of theIP-seq experiment in order to determine the transcription factor binding site of the transcription factor of interest
- Probe: Information about the probe
- Treatment: Information about the treatment (data from H.sapiens experiments, source ENCODE)
- Replicate: Information about the replicates (source ENCODE)
- List Hits: number of genes, belonging to the uploaded list, which have the specified trascription factor binding site in the promoter region
- Genome Hits: number of genes, belonging to the genome, which have the specified trascription factor binding site in the promoter region
- Target Genes: Gene names of the List Hits genes
- Score: Score of the hypergeometric test computed as: (List Hist/List Size)/(GenomeHits/Genome Size)
- P-value: p-value of the hypergeometric test
- FDR: adjusted p-value (Benjamini-Hochberg)
- combined-score: score * -log10(p-value)
The datatable is fully responsive: can be ordered, it's possible to search for genes/transcription factor of interest among the results, directly check the target genes of specific transcription factor and hovering with the mouse on the field of interest you can have a short description of the meaning of each value.
OSS. The statistical test is done based on all the transcripts belonging to each gene. For this reason the Genome size and the List size will be bigger then, respectively, the Genome of the organism of interest and the uploaded list.
For each function, once the user will have selected the region of interest, will be generated a downloadable table containing the respective genes and transcripts.
Moreover it is a resposive table: can be ordered, it's possible to search for genes of interest among the results, and also, with a click on the gene of interest the user will be redirected to the respective selected resource
Optionally, this table will also be annotated with the data contained in the user provided custom annotation file.