![ortholog layout in cytoscape ortholog layout in cytoscape](https://i1.wp.com/www.researchstash.com/wp-content/uploads/2019/09/Cytoscape.png)
This is the FDR calculated by the TOMTOM p-value for the similarity of "N/A" indicates that orthology identity is not used (e.g. But when the threshold is set to zero, no orthologous information is used. The closer the score to zero, the more homologous genes can be associated to anĪnnotated TF. This %identity was calculated in EnsemblCompara gene trees based on whole amino acid sequence alignments Right-click on it, and click on details to get more description about the motif2TF prediction. Gene ID of the predicted Transcription Factor Right-click on the logo image to save it to PNG file. Name and link to the source database when possible is added to The motif from the selected row is displayed as a motif logo (see weblogo). This column indicates the number of TFs that can be associated by the motif2TF algorithm to the given This column indicates the number of target genes selected for the given motif.
#Ortholog layout in cytoscape code
Cluster code starting by "M" corresponds to motif cluster and code with "T" to track cluster. The cluster code is given by order of maximal Have the same cluster code and the same background color. The enriched motifs are clustered by similarity and similar motifs that belong to the same cluster will The AUC is usedįor the calculation of the enrichment score Cluster Code This is the Area Under the Curve that is calculated in the cumulative enrichment plot. This column corresponds to the enrichment score of the motif or the maximal enrichment score for a given transfac_pro,įlyfactorsurvey) and the source ID of the motif. In general, it corresponds to the source motif database (e.g. This column corresponds to the rank according to the NES score. The filtered rows on top or bottom of the table. By clicking on the column name, the results will be sorted with The results having the relevant information Circular layout is applied when a new network is drawn or if current network has no edges. Edges corresponding to the same cluster have The interactions areĭrawn with directed edges from the TF to the target genes. This style draws all target genes as pink ellipses. Edges corresponding to the same motif have This style draws all target genes as squares.
![ortholog layout in cytoscape ortholog layout in cytoscape](https://apps.cytoscape.org/media/kgmlreader/screenshots/kgml_ss1.png)
This button will close the current results tab and will ask if the user wants to save the results. This button will export the results in a tab-delimited text file (.txt). This button will save the results in the iRegulon format (.irf). This button will import the results in the iRegulon format (.irf). Information will be checked in the filter column of the main view table (TF Table in TF view or Motif This menu allows the search of a motif, TF or target gene in the results. This menu will show the selected TF and will allow the user to scroll over the predicted TFs. Warning! Notice that for the moment this option is not available yet in the Cytoscpae 3.1.x version of the plugin. The new network will keep the same layout, but the motif information is lost with the edge This option will create a new network with the merge of all TF-target gene interactions (one edge perĮach). This option will allow the user to query the metaregulons of the selected TF using our TF-Target database(see query). This is visualised in the iRegulon Visual Style. Also the interaction between these (between the Transcription factor and all target genes will be shown. Is the name of the selected transcription factor with the name of the selected motif. This option will create a new window in the view, and create a new network. This option will add all the target genes and the selected transcription factor to the current network.Įdges will be add to the network between the transcription factor and the target genes. Seen when the user put the mouse over this title. On the top left, of the Tool panel is the name of the analysis. Heads Up! In motif2TF Table and Target Selection Table, the genes that are already in the