Queensland University of Technology QCIF QCloud TRNDiff Regulon Browser

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Introduction

TRNDiff is a node.js app which exists to support visual comparison of transcriptional relationships across dozens or even hundreds of organisms. We use a simple, compact 'wagon wheel' representation of the Transcriptional Regulatory Network (TRN), centred on a single Transcription Factor (TF). Here the wagon wheel hub is the TF, and the possible target genes (TGs) appear as nodes on the wheel rim. A regulatory relationship is shown by a spoke between the hub and the node.

Quick Start

Step 1: Choose a data source

There are three options:

  1. RegPrecise Genomes: connect to RegPrecise and browse by Genomes.
  2. RegPrecise Regulogs: connect to RegPrecise and browse by transcription factors (regulogs).
  3. Local File: upload local data

Step 2

Only for options 1 and 2 from Step 1 (RegPrecise). Follow the substeps to drill down to collection for browsing.

For example, if you selected option 1 RegPrecise Genomes, then you will need to:

  1. Select Genome from the table (next step is automatically shown)
  2. Select Regulon for the chosen genome
  3. View Regulog will show the 'wagon wheels'

Option 2 will have a different set of sub options. See our website for more details.

Other features

There are also other functions available with TRNDiff:

  • Clustering/grouping
  • Comparisons
  • Highlight by functional GO terms
  • Searching by free text
  • Uploading local data - see format

Visit our website, trndiff.org for more information.

About RegPrecise

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.


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 E/H ratio Save to CSV Toggle colour blind
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off Toggle colour blind
Regulon 1:
Regulon 2:
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 E/H ratio Save to CSV Toggle colour blind
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off Toggle colour blind
Regulon 1:
Regulon 2:
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 E/H ratio Load CSV Save to CSV Toggle colour blind
Icon list Small overview Large overview Detail view Clear selection Highlight GO term Highlight search Comparison lock off Toggle colour blind
Regulon 1:
Regulon 2: