Table 1.
Metabolic Networks and Pathway Analysis Tools
| Tool | Applications in endocrine disorders and cancer | |
|---|---|---|
| Metabolic network reconstruction | Metabolic reconstructions (e.g., Recon3D [96]) | Provides a detailed metabolic network model for studying metabolic alterations |
| Supports integration of multi-omics data | ||
| Human Metabolome Database (HMDB [97]) | A valuable resource for annotating metabolomics data and linking metabolites to pathways | |
| KEGG (Kyoto Encyclopedia of Genes and Genomes [98]) | Provides a wide range of metabolic pathway maps and gene annotations | |
| HumanCyc [99] | Provides a comprehensive collection of metabolic pathways and enzymatic reactions in humans | |
| Biochemical Genetic and Genomic (BiGG) models [100] | Offers a repository of curated metabolic models for various organisms | |
| Metabolic network analysis tools | Constraint-Based Reconstruction and Analysis (COBRA) toolbox [101] | Allows constraint-based modeling and flux analysis of metabolic networks |
| Pathway tools [102] | Software for pathway/genome databases and systems biology research that supports the construction and visualization of metabolic pathways | |
| Isotopomer Network Compartmental Analysis (INCA 2.0) [103] | Software that performs steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis | |
| Metran [104] | Software for performing 13C-metabolic flux analysis, tracer experiment design, and statistical analysis | |
| 13CFLUX2 [105] | Facilitates the measurement and modeling of carbon fluxes in metabolic pathways in vivo | |
| mfapy [106] | Offers a user-friendly interface for performing flux balance analysis and metabolic modeling, focusing on data analysis procedures | |
| Pathway enrichment analysis | MetaboAnalyst [107] | Facilitates pathway enrichment analysis using metabolomics data |
| Database for Annotation, Visualization, and Integrated Discovery (DAVID) [108] | Useful for gene enrichment analysis to identify overrepresented pathways and functions | |
| Enrichr [109] | Performs gene set enrichment analysis (GSEA) to identify enriched pathways and processes | |
| Metabolomics Pathway Analysis (MetPA) tool [110] | Focuses on the interpretation of metabolomics data in the context of metabolic pathways | |
| Network visualization | Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) [111] | Provides protein-protein interaction networks, helping visualize connections between genes and proteins |
| OmicsNet [112] | Integrates multi-omics data (e.g., genomics, proteomics, metabolomics) and visualizes molecular interactions | |
| Cytoscape [113] | Helps visualize metabolic networks and omics data in a network context | |
| MetExplore [114] | Facilitates the visualization and interpretation of metabolomics data in the context of genome-scale reconstructed metabolic networks |