Identification of Transcriptional Regulatory Interactions

Welcome & What can we offer

Laboratory of bioinformatics of the Institute of Microbiology ASCR, v.v.i. focusses, within the frame of C4Sys infrastructure, on the inference and modeling of cell regulatory systems. For this purpose, we have been developing algorithms for identification of transcriptional regulatory interactions. These algorithms were originally applied on model organisms as yeast and prokaryotic antibiotic producers of the streptomycetes genus. The algorithms have mainly been coded in Matlab, within its environment. A program for simulation of genetic networks GenExp was created as a user interface driven Matlab application and can be downloaded from our web server. Currently we have finished an app for inference of gene regulatory interactions running under Cytoscape – one of the most important collection of tools for systems biology. The app can be downloaded from the link below.

During last years, we focused on construction of a pipeline of laboratory protocols and computational programs for inference of gene regulatory networks with main focus on prokaryotes. The pipeline consists in protocols for creation of mutants with specifically tagged regulator gene (sigma factor in particular), followed by immunoprecipitation of fragmented DNA and protocols for their sequencing in ChIP-seq scheme. The sequencing data are then processed in a pipeline of procedures for quality control, significance analysis and mapping on genome. The procedure is accompanied with RNA-seq or microarray based acquisition of time series of gene expression. Both Chip-seq results and time series are processed in the software mentioned above, that allows to identify regulatory interactions active during the process recorded in the time series of gene expression.

How can you access

Head of the lab: Jiří Vohradský,

CyGenexpy and sw development responsible: Martin Černý,

Epitope tagging and ChIP-seq analysis, scanning: Alice Ziková,


Inference and simulation of gene expression networks:

GenExp –

Matlab environment procedure for simulation of gene expression networks.

CyGenexpi –

A Cytoscape plugin for inference of gene expression networks from binding data and gene expression time series.

Both tools are freely accessible.

Epitope tagging based ChIP-seq analysis

Assistance in creation of specific protocols for obtaining binding data for sigma factors of prokaryotes.

Training on the software tools

Radio- and fluorescent labeled images scanning service.

Freely available service for scanning and image processing of labeled images. Originally intended for 2DE electrophoresis for which we can offer processing in pdQuest software. Generally, the scanning facility is not restricted to a specific type of image templates, it is based on a BioRad Molecular Imager FX scanner with additional laser, covering most of the dyes spectra, including phosphor imaging plates.