Queensland University of Technology QCIF QCloud TRNDiff Regulon Browser

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About Instructions

Introduction

The advent of next generation sequencing technologies has seen explosive growth in genomic data, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. The challenge thus lies in comparing models of complex relationships, were once restricted to a single genome, across hundreds of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis requires simultaneous displays of multiple networks well beyond those of existing network visualisation tools (Gehlenborg et al., 2010). TRNDiff supports the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations across strains.

Reconstructing TRNs based on the Regulog approach

A widely used assumption to infer regulatory interactions follows: given a known interaction between a TF and TG in a model system, if both the orthologous TF and TG are found in a target genome, then it is assumed the orthologous TF regulates the orthologous TG (citation). This is referred to as the regulog assumption. Traditional regulatory network structures based on this approach display an edge to represent the regulatory relationship. However, this approach does not take into account the identification of transcription factor binding sites (TFBSs), which is becoming the standard approach. We include TFBSs in our construction when visualising such regulatory networks.

Browsing the RegPrecise database

RegPrecise [http://regprecise.lbl.gov/RegPrecise/] is a repository of high-quality reference data which captures the regulatory relationships between genes in 390 prokaryote genomes. The database contains manually curated details of genes, transcription factors and transcription factor binding sites which have been obtained by careful comparative genomic analysis, experimentation and literature review as outlined in the paper:

Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 January; 38(Database issue): D111–D118.

TRNDiff is intended to provide an easy way to browse the RegPrecise database, locate a regulog of interest, and view the regulons belonging to the regulog. Any regulog can be saved to the desktop in CSV format, and these files can be edited and then reloaded into the program to view the results.

Future versions of this application will provide further integration of TRNDiff and RegPrecise with standard tools such as NCBI BLAST to allow users to execute more powerful workflows.

Contact us

Please direct any enquiries to the project leader, James Hogan, at j.hogan@qut.edu.au.


Navigating RegPrecise

The fundamental organising principle of RegPrecise is the regulon, which represents a set of co-regulated genes in the genome of a single bacterial species. A regulon consists of a transcription factor together with the collection of genes regulated by the transcription factor and the sites at which the transcription factor binds to the DNA strand upstream of each regulated operon. Regulons from multiple organisms are grouped to form regulogs. A regulog is an equivalence class of regulons in which all transcription factors are orthologous. RegPrecise provides further levels of organisation by gathering regulogs into collections based on taxonomic grouping, transcription factor family, RNA family, pathway and effectors. In addition, RegPrecise organises regulons by the organism from which they originate.

TRNDiff provides two major navigational paths through RegPrecise.

  • The RegPrecise Genomes panel is intended for locating regulons contained in specific organisms, and branching out from there to to obtain corresponding regulons (if any) in the other organisms in the collection. The panel contains three pages:
    • 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.

      Click an item in the table to browse any regulons that have been annotated in the corresponding genome.

    • 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.

    • 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.

      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.

    • Regulon Comparison displays a variant of the normal reuglog view which performs logical comparisons between pairs of regulons.

      The Regulon 1 and Regulon 2 boxes are used to choose the two regulons to compare. This defaults to the first two regulons in the regulog. The wagon-wheel representation of AND, OR and XOR logical operations will be displayed for the selected regulons, combined into one wagon-wheel for each comparison.

      If more than two regulons have been compared, these two boxes will be replaced by a Referencebox, which instead allows the reference regulon of the current comparison to be changed. A button will also appear that will reset the comparison to the default two network comparison.

      Selecting regulons in the main view will normally alter the comparison view to compare the selected regulons. If more than two were selected, the first selected regulon will act as the reference regulon, while all other selected regulons will be compared against it in a OR logical operation. To disable this behaviour, the Comparison lock option can be toggled.

      Clear Selection, Highlight GO Term, Highlight Search and Zoom Level options will operate the same as in the normal display.

  • The RegPrecise Regulogs panel allows browsing the various regulog collections to locate regulons.
    • Select Regulog Collection allows the selection of a regulog collection type (one of Taxonomic Group, Transcription Factor, Transcription Factor Family, RNA Family, Pathway or Effector) to display a table containing summary information about the available regulog collections of that type.

      The table may be sorted in ascending or descending order by clicking on any of the column headings.

      Click an item in the table to browse the regulogs belonging to the collection.

    • Select Regulog shows a table containing summary information about the regulogs in the selected collection.

      A page navigation control above the table enables navigating through collections without needing to return to the SSelect Regulog Collection page.

      Click an item in the table to view the regulog that contains the corresponding regulon.

    • View Regulog and Regulog Comparison in this panel behave in much the same way as they do in the RegPrecise Genomes panel.

Working with local data

The Local Regulogs panel allows a regulog collection to be loaded from the local device and displayed in the application.

The regulog collection should be formatted in the same manner as a collection saved by the Save Regulog function in the other panels.

The document is organised as a sequence of blocks with the following structure:

[optional blank lines]
TableName
[one blank line]
ColHeading,ColHeading,ColHeading,...
RowData,RowData,RowData,...
... 
RowData,RowData,RowData,...
[at least one blank line]

Valid table names and column headings are set out in the following table.

Table Name Column Headings
Regulogs effector, regulationType, regulatorFamily, regulatorName, regulogId, taxonName, pathway, numGroups
Regulons regulonId, regulogId, genomeId, genomeName, regulatorName, regulatorFamily, regulationType, effector, pathway, groupNumber
Genes regulonId, vimssId, name, locusTag, geneFunction, goTerm
Regulators regulonId, vimssId, name, locusTag, regulatorFamily
Sites geneLocusTag, geneVIMSSId, position, regulonId, score, sequence
Select Genome Select Regulon View Regulog Regulon Comparison
Available model organisms
Filter:
RegPrecise Id Name Taxonomy Id TF Regulon Count TF Site Count RNA Regulon Count RNA Site Count
Page selection control.
Filter:
RegulogId Regulation Type Effector Regulator Family Regulator Name Pathway
Page selection control.
Icon list Small overview Large overview Detail view Sort regulons Clear selection Highlight GO term Highlight search Change number of groups Auto grouping on Recalculate groups Auto centroid off Save to CSV
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off
Regulon 1:
Regulon 2:
Select Regulog Collection Select Regulog View Regulog Regulon Comparison
Collection type:
Filter:
Collection Id Class Name Name
Page selection control.
Filter:
RegulogId Taxon Regulation Type Effector Regulator Family Regulator Name
Page selection control.
Icon list Small overview Large overview Detail view Sort regulons Clear selection Highlight GO term Highlight search Change number of groups Auto grouping on Recalculate groups Auto centroid off Save to CSV
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off
Regulon 1:
Regulon 2:
View Regulog Regulon Comparison
Page selection control (local).
Icon list Small overview Large overview Detail view Sort regulons Clear selection Highlight GO term Highlight search Change number of groups Auto grouping on Recalculate groups Auto centroid off Load CSV
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off
Regulon 1:
Regulon 2: