Section 7.3 (pathway and network solutions)

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capture_7.3 MS-DIAL LipidSig 2.0 LipidOne Lipostar 2.0 WikiPathways (lipid portal) BioPAN
Input style MzML, cdf, abf, hive, sciex, waters, bruker, shimadzu, thermo, agilent CSV, TSV, XLSX Txt, csv .d(Agilent), .d(Bruker), Shimadzu, .raw(Thermo), .raw(Waters) GPML CSV
Pathways — — Not applicable 13 maps available, mainly covering GL, GP, FA (including eicosanoids), SL, ST (including bile acids) Lipid metabolic pathways including lipid biosynthesis and remodelling (e.g. sphingolipid metabolism) Main lipid biosynthesis and remodelling pathways (e.g. de novo lipogenesis, de novo sphingolipids, and cholesterol biosynthesis).
Species — LipidSig is not restricted to a specific species. Homo_sapiens, Mus_musculus, Rattus_norvegicus, Canis_lupus_familiaris, Sus_scrofa, Xenopus_tropicalis, Arabidopsis_thaliana, Saccharomyces_cerevisiae, Drosophila_melanogaster, Danio_rerio — Human, mouse (and >20 other, not all covering lipids) Mammals (user can make use of biochemistry and lipid metabolism to check if obtained genes are conserved across species).
Pathway editing No No No No No No
Pathway mapping No Https://lipidsig.bioinfomics.org/Tutorial/?Network Internal database (published) Yes Pathway browsing, searchable by species, keywords. Pathway reactions are classified as activated or suppressed using a Z-score based on the mean and standard deviation of lipid quantities, used to rank reactions and identify significant changes between control and treated conditions.
Visualisation Molecular spectrum networking LipidSig 2.0 supports visualization of differential expression results (volcano and lollipop plots), characteristic-based lipid patterns, correlation analyses, enrichment results, machine-learning outputs, and multiple metabolic network views including reaction networks, pathway activity maps, and GATOM subnetworks. All visual outputs are publication-ready and downloadable. No Interactive pathway graphs Interactive pathway graphs comprising involved lipids and genes/proteins Interactive pathway graphs comprising regulated lipids and reactions; available at lipid subclass, lipid molecular species, and fatty acid levels
Links to related gene proteins No Https://lipidsig.bioinfomics.org/Tutorial/?Network No Yes Related genes/proteins with links to UniProtKB, GO, WikiGenes identifiers Predicted genes