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Pipeline publication

[…] ], PathWhiz [], and Interactive Pathways Explorer (iPath) []. They can often provide some kind of pathway structure analysis such as PathVisio [], Functional Enrichment Analysis Tool (FunRich) [], BiNChE [], and Metabolite Pathway Enrichment Analysis (MPEA) [] that uses pathway enrichment analysis and pathway activity profiling [] that calculates pathway activity scores to represent the potential metabolic pathway activities and performs statistical analysis to investigate differences in activity between conditions. Tools like Integrated Analysis of Cross-Platform Microarray and Pathway Data (InCroMAP) [], Integrated Interactome System (IIS) [], Kazusa Plant Pathway Viewer (KaPPA-View4) [], MapMan [], ProMeTra (which is integrated with MeltDB 2.0) [], Paintomics [], Visualization and Analysis of Networks Containing Experimental Data (VANTED) [], MBROLE [], and Integrated Molecular Pathway Level Analysis (IMPaLA) [] go 1 step further and integrate metabolomics processed data with other omics platforms, particularly transcriptomics, providing analysis and visualization of large integrated datasets to assist data interpretation., Few tools try to actually use mass spectra features to build the networks, which can also improve annotation of unknown compounds. MetaNetter [] uses raw high-resolution data and a list of potential biochemical transformations to infer metabolic networks. MetaMapR [] builds chemical and spectral similarity networks […]

Pipeline specifications

Software tools MapMan, ProMeTra, MeltDB, Paintomics