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.
There are three options:
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:
Option 2 will have a different set of sub options. See our website for more details.
There are also other functions available with TRNDiff:
Visit our website, trndiff.org for more information.
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.
Please direct any enquiries to the project leader, James Hogan, at firstname.lastname@example.org.