Analyzing and interpreting genome data at the network level with ConsensusPathDB

作者：Herwig, Ralf^*; Hardt, Christopher; Lienhard, Matthias; Kamburov, Atanas^*

来源：Nature Protocols, 2016, 11(10): 1889-1907.

DOI：10.1038/nprot.2016.117

• PROTEIN INTERACTIONS
• UREMIC TOXINS
• GENE
• EXPRESSION
• DIFFERENTIATION
• CLASSIFICATION
• INDIVIDUALS
• INHIBITION
• METABOLISM
• SIGNATURES

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.

• 出版日期2016-10