ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB (http://consensuspathdb.org) with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.

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Motivation: Extensive drug treatment gene expression data have been generated in order to identify biomarkers that are predictive for toxicity or to classify compounds. However, such patterns are often highly variable across compounds and lack robustness. We and others have previously shown that supervised expression patterns based on pathway concepts rather than unsupervised patterns are more robust and can be used to assess toxicity for entire classes of drugs more reliably.Results: We have developed a database, ToxDB, for the analysis of the functional consequences of drug treatment at the pathway level. We have collected 2694 pathway concepts and computed numerical response scores of these pathways for 437 drugs and chemicals and 7464 different experimental conditions. ToxDB provides functionalities for exploring these pathway responses by offering tools for visualization and differential analysis allowing for comparisons of different treatment parameters and for linking this data with toxicity annotation and chemical information.Database URL: http://toxdb.molgen.mpg.de

BackgroundModern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays. XML has become the most prominent format for representing and exchanging these data. However, besides the development of standards there is still a fundamental lack of data integration systems that are able to utilize these exchange formats, organize the data in an integrative way and link it with applications for data interpretation and analysis.ResultsWe have developed DIPSBC, an interactive data integration platform supporting collaborative research projects, based on Foswiki, Solr/Lucene, and specific helper applications. We describe the main features of the implementation and highlight the performance of the system with several use cases. All components of the system are platform independent and open-source developments and thus can be easily adopted by researchers. An exemplary installation of the platform which also provides several helper applications and detailed instructions for system usage and setup is available at http://dipsbc.molgen.mpg.de.ConclusionsDIPSBC is a data integration platform for medium-scale collaboration projects that has been tested already within several research collaborations. Because of its modular design and the incorporation of XML data formats it is highly flexible and easy to use.

Objective Physical exercise training is associated with increased glucose uptake in skeletal muscle and improved glycemic control. HDAC5, a class IIa histone deacetylase, has been shown to regulate transcription of the insulin-responsive glucose transporter GLUT4 in cultured muscle cells. In this study, we analyzed the contribution of HDAC5 to the transcriptional network in muscle and the beneficial effect of muscle contraction and regular exercise on glucose metabolism. Methods HDAC5 knockout mice (KO) and wild-type (WT) littermates were trained for 8 weeks on treadmills, metabolically phenotyped, and compared to sedentary controls. Hdac5- deficient skeletal muscle and cultured Hdac5- knockdown (KD) C2C12 myotubes were utilized for studies of gene expression and glucose metabolism. Chromatin immunoprecipitation (ChIP) studies were conducted to analyze Il6 promoter activity using H3K9ac and HDAC5 antibodies. Results Global transcriptome analysis of Hdac5 KO gastrocnemius muscle demonstrated activation of the IL-6 signaling pathway. Accordingly, knockdown of Hdac5 in C2C12 myotubes led to higher expression and secretion of IL-6 with enhanced insulin-stimulated activation of AKT that was reversed by Il6 knockdown. Moreover, Hdac5 -deficient myotubes exhibited enhanced glucose uptake, glycogen synthesis, and elevated expression levels of the glucose transporter GLUT4. Transcription of Il6 was further enhanced by electrical pulse stimulation in Hdac5 -deficient C2C12 myotubes. ChIP identified a ∼1 kb fragment of the Il6 promoter that interacts with HDAC5 and demonstrated increased activation-associated histone marker AcH3K9 in Hdac5 -deficient muscle cells. Exercise intervention of HDAC5 KO mice resulted in improved systemic glucose tolerance as compared to WT controls. Conclusions We identified HDAC5 as a negative epigenetic regulator of IL-6 synthesis and release in skeletal muscle. HDAC5 may exert beneficial effects through two different mechanisms, transcriptional control of genes required for glucose disposal and utilization, and HDAC5-dependent IL-6 signaling cross-talk to improve glucose uptake in muscle in response to exercise.