Elucidating gene regulatory network (GRN) from large scale experimental data remains a central challenge in systems biology. The advent of high-throughput data generation technologies has allowed researchers to fit theoretical models to experimental data on gene-expression profiles.
Offers a component-based architecture that allows users to add new functionality in the form of plug-in modules. geWorkbench includes many computational resources permitting to delete many steps that require programming skills. It simplifies the utilization of multi-module analysis pipelines. The tool’s modules consist of wrapped versions of pre-existing third-party software tools.
Allows gene set or pathway analysis. GAGE is able to reveal novel and relevant regulatory mechanisms from microarray studies. It produces good results concerning consistency across parallel studies or experiments; sensitivity and specificity of the pathway inference and biological relevance of the pathways identified. The tool compare expression level changes of a gene sets to the whole set background by using a two-sample t-test.
Provides comparative analysis of microbial regulons. RegPredict is a highly interactive web server specifically designed for identification of Transcription Factor Binding Sites (TFBSs). This server has a user-friendly interface and multiple functionality including: (i) scanning of microbial genomes with annotated DNA motifs and collections of aligned binding sites, (ii) collecting upstream DNA regions for any gene set and identification of novel TFBS motifs and (iii) comparative analysis of the genomic context of candidate TFBSs in the group of genomes.
Provides methodology to infer direct regulatory relationships between transcriptional regulator proteins and target genes. ARACNE is a program that can be used for reconstructing context-specific transcriptional networks in multiple tissue types. Moreover, it permits researchers to determine novel driver genes and mechanisms as well as drug mechanisms of action.
Infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. MERLIN is an algorithm for learning regulatory networks that strikes a balance between per-gene and per-module methods. It was used to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation.
A regulon consists of a transcription factor (TF) and its direct transcriptional targets, which contain common TF binding sites in their cis-regulatory control elements. The iRegulon plugin allows you to identify regulons using motif and track discovery in an existing network or in a set of co-regulated genes.
Infers relations between genes from mutant-based experiments. GenePath is based on principles of epistasis analysis. It can assist biologists in the systematic exploration of mutant data, in identifying and testing new relations, and in documenting and communicating genetic data. It can also help in teaching concepts of genetic data analysis. Examples are provided, including gene network studies on Dictyostelium discoideum (transition from growth to development, spore formation and intercellular communication) and Caenorhabditis elegans (programmed cell death and dauer larva formation).