Project Overview

Objectives
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Intuitive network visualization in 2D or 3D space
A Graph File
[ network visualization ]
Link microbiome, SNPs or MS peaks to knowledge framework
Taxon List
[ microbiome to metabolites ]
LC-MS Peaks
[ peaks to metabolites ]
SNP List
[ variants to genes ]
Systems analysis of one or more list(s) of molecules
Gene List
[ protein-protein interactions ]
Protein List
[ protein-protein interactions ]
Transcription Factors
[ TF-gene interactions ]
miRNA List
[ miRNA-gene interactions ]
Metabolite List
[ metabolite reactions ]

News & Updates

  • Updated tutorials for MS peak and taxon list inputs (01/21/2022);
  • Improved SNP-gene mapping functions for better performance (01/18/2022);
  • Enhanced LC-MS peak-to-metabolite interface for better user experience (01/12/2022);
  • Code refactoring and bug fixing based on user feedback (01/07/2022);
  • Added support for microbiome metabolite prediction based on comprehensive genome-scale metabolic models (GEMs) (12/20/2021);
  • Upgraded to PrimeFaces 11 (12/18/2021);
  • Added support for global annotation of untargeted metabolomics data based on the NetID approach (12/10/2021);
  • Code cleaning and interface updates (10/15/2021);
  • Added support for topological distributions in Network Tools (09/15/2021);
Read more ......

Citing OmicsNet

  • Zhou, G. and Xia, J. (2018) "Using OmicsNet for Network Integration and 3D Visualization" Current Protocols in Bioinformatics (doi:10.1002/cpbi.69).
  • Zhou, G. and Xia, J. (2018) "OmicsNet - a web-based tool for creation and visual analysis of biological networks in 3D space" Nucleic Acids Research (doi:10.1093/nar/gky510).
Upload a list of genes
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Upload a list of proteins
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Upload aa list of miRNAs
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Upload a list of metabolites
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Upload a list of SNPs
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Upload a list transcription factors
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Upload a Graph File
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A small network (.json)
A medium network (.txt)
A large network (.graphml)
Upload and process peak list file
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(editable)
(editable)
None
Malaria (ESI+)
Upload a list of taxon names
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