Two queries are available from iRegulon plugin with their corresponding parameters discussed here in this manual.
Enter a name for your analysis, it will be used to name your results and will be suggested for saving the results.
This is the species and the gene nomenclature. All the possible species and there nomenclature that can be used is shown here. Currently these are:
Select a TF in a list of 886 TFs with precalculated TF-targets (metaregulons).
Choose the node attribute that represents the gene name. The selected attribute must be in a supported format (see Species & Gene Nomenclature).
This is the number of selected nodes with valid gene names. If it is zero, it means that the user forgot to select the nodes before using the query panel.
This parameter allows to define the type of the regulatory search space from:
If several motif/track collections are available, use this parameter to select one motif/track collection. More details about our collections here.
This parameter delineates in more detail the search space, i.e. the putative regulatory region.
According to the type of the search space and the putative regions, several databases can be queried:
This parameter allows the user to query the metaregulons across the results of the run of iRegulon on several databases of known signatures:
You can select one or multiple databases.
The three following parameters are specific to region-based databases (i.e., not available for gene-based search space).
This is the fraction of the putative regulatory region associated with a gene that must overlap with the predefined regions. This parameter must be between 0 and 1.
You can select a predefined regulatory search space or specify here the size of the region (in bp) upstream of the TSS to use in the mapping to predefined regions.
You can select a predefined regulatory search space or specify here the size of the region (in bp) downstream of the TSS to use in the mapping to predefined regions.
This is the minimal NES score to consider a motif as being relevant. The default score threshold is set to 3. This score corresponds to a FDR on the TF recovery between 3% and 9% (when validated on ENCODE ChIP-seq datasets using different regulatory search spaces).
The Area Under the Curve (AUC) values are calculated for all motifs at the beginning of the cumulative gene recovery plot (aka ROC curve) which plots the input gene recovery along the whole genome ranking. This threshold indicates the percentage of the top ranked genes/regions to consider for the AUC calculation (3% => 420 genes in the gene based ranking).
This is the x-axis cutoff for visualization of the ROC curve (see above). This value corresponds with the top genes shown on the results.
This is a threshold on the miniminal identity score to define gene orthology. This %identity was calculated in EnsemblCompara gene trees based on whole amino acid sequence alignments (tf2tf associations). The closer the score to zero, the more homologous genes can be associated to an annotated TF. But when the threshold is set to one, no orthologous information is used. This score must be between 0 and 1.
This is a threshold on the maximal FDR calculated by the TOMTOM p-value for the similarity of the motifs (motif2motif associations). The closer the score to zero, the more similar motifs will be selected for association to a enriched motif. But when the threshold is set to zero, no motif similarity information is used. The score must be between 0 and 1.
This is a threshold on the minimum occurrence of the target genes. In a meta-targetome, each target gene is annotated with a number that represents the number of gene sets where the TF is found enriched and the gene is among the optimal subset of direct targets.
This is a threshold on the approximate number of targets to be displayed for a calculated metatargetome. The targets with the same score of the target at the threshold will be also displayed.
If the user tick this option, a new network will be created in cytoscape. Otherwise, the network will be added to the current window.
