Navigating with RegPrecise Genomes

RegPrecise Genomes

The panel contains four pages:

  1. Select Genome
  2. Select Regulon
  3. View Regulog
  4. Regulon Comparison (see Making comparisons)

Select Genome

The Select Genome shows a table containing summary information about all the genomes for which annotations are available in the database.

  • The table may be sorted in ascending or descending order by clicking on any of the column headings.
  • The Filter box can be used to restrict the view to records containing particular text in the organism name. To do this, enter the text in the box and click the Search button. To restore the view to all records, clear the text from the Filter box and click Search.
  • You can click an item in the table to browse any regulons that have been annotated in the corresponding genome.

Example of the Select Genome page in TRNDiff

Select Regulon

The Select Regulon shows a table containing summary information about the regulons in the selected genome. A page navigation control above the table enables navigating through genomes without needing to return to the Select Genome page. Click an item in the table to view the regulog that contains the corresponding regulon.

Example of the Select Regulon page in TRNDiff

View Regulog

The View Regulog displays a graphical view which allows examination cross-species regulatory conservation within a group of related organisms.

The view consists of a set of wagon-wheel constructs, one for each regulon. Each wheel has a central node and a set of nodes laid out on the perimeter of a circle. The central node represents the regulator while the others represent the regulated genes. A solid line joins the regulator to a gene on the perimeter if a binding site has been recorded for the gene. A dashed line indicates that no binding site annotation is available.

Example of the View Regulog page in TRNDiff

The angular position of each gene is determined by grouping the genes across all regulons into sets of orthologs. The member genes of each set of orthologs are placed at the same angular location in their respective regulon.

Genes can be selected by clicking on the nodes, where they will be highlighted by a blue outline. Homologs of that gene across the rest of the regulons will also be highlighted. Clicking on the node again will deselect it and its homologs. Regulons can also be selected by clicking on the background - selected regulons appear with a grey background.

A page navigation control above the table enables navigating through regulogs without needing to return to the Select Regulon page.

There are four zoom levels available, selected from the Zoom Level box:

  • Icon List: Displays each regulon in a labelled icon form
  • Small Overview: The default zoom level, displaying each regulon in a small size
  • Large Overview: Displays each regulon in a larger size
  • Detail View: The largest size, with gene names beside each gene in the reuglon. If any regulons were selected in the view, the detail view will only show those specific ones. In group mode, the groups will be hidden if only a selection of regulons is being viewed.

The Highlight GO Term button will display a drop down menu that allows the selection of a high-level molecular function. All genes in the display that belong to the selected category will be highlighted in the display.

The Highlight Search button will allow searching for a query term within the fields of all genes of the current regulog. The search will look at a gene's name, GO term, RegPrecise gene function, annotation or sequence. Any genes that contain the query string (not case sensitive) in one of those fields will be highlighted.

The Clear Selection button will clear any selected and highlighted genes in the current display.

The Save Regulog button allows the current regulog to be saved to a computer for editing. The file is saved as a single Comma-Separated Values (CSV) file which may be edited in a spread sheet program for editing. Files saved and edited in this way may be viewd with the Local Regulogs panel.

Regulons can also be seperated into groups by choosing a number of groups greater than one from the Change Number of Groups button. If Automatic Grouping is enabled, regulons will be automatically assigned into groups based upon a K-means clustering algorithm, using both Hamming and Eucildean distances. If it is disabled, regulons will not change position and the user may place them in groups manually. With automatic grouping enabled, the Recalculate Groups button will redo the grouping process.

Centroids are indicated by a blue border around the regulon (and are also visible in a single-group display), and after an automatic grouping, the final centroids from the clustering will be shown. When regulons are then dragged between groups, enabling the Auto Centroid function will automatically recalculate the centroid for all groups affected by the drag-and-drop operation. Any centroids that were changed by the recalculation will flash blue.

Because of the random selection of centroids when performing K-means clustering, each grouping will likely be different. Automatic grouping is meant to be a suggestion only for the user, and shouldn't be taken as the only possibility.

In both single- and multi-group displays, regulons can be repositioned by dragging and dropping them around the interface. They can be placed anywhere inside the container. If grouping is enabled, the group a regulon is in will be calculated on drop, dependant on the location of the centre of the regulon's bounding box. The sorting function allows the user to order the regulons with the given filters, and automatically takes groups into account. Any manual positioning will be lost when sorting.