Integrating multi-omics data via knowledge-based networks
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Genes

  • ID types: Entrez, Ensembl, Uniprot, KO or gene symbol

Proteins

  • ID types: Ensembl, Uniprot, Gene symbol

Transcription factors

  • ID types: Entrez, Ensembl, Uniprot or gene symbol

miRNAs

  • ID types: miRBase Accession or miRBase ID

Metabolites

  • ID types: KEGG ID, HMDB ID or PubChem ID

Graph file

  • Formats: .sif, .graphml, .json or .txt (edge list)
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News & Updates
  • Consolidated interface and functions between 2D and 3D network visualization (06/08/2021);
  • Fixed the issue in creating secondary network and improved 2D network visualization (06/02/2021);
  • Upgraded to PrimeFaces 10 (04/27/2021);
  • Bug fix for network upload and enrichment analysis (03/22/2021);
  • Added support for node and edge adding feature (02/18/2021);
Read more ......

Project Objectives

OmicsNet has been developed to address three needs: 1) systems analysis of a single list of molecules; 2) integrative analysis of multiple lists of different types of molecules; and 3) intuitive web-based 2D/3D visualization. OmicsNet supports four types of molecular interactions - PPI, TF-gene, miRNA-gene and metabolite-protein. The 3D network visualization was implemented based on the innovative WebGL technology. Users can perform various style customization, enrichment analysis, targeted interactor search, and network toplology analysis for hypothesis generation and systems-level insights.

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).
Gene List Upload
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Protein List Upload
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miRNA List Upload
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Metabolite List Upload
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Transcription Factor List Upload
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Upload a Graph File
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A small network (.json)
A medium network (.txt)
A large network (.graphml)
WebGL Support Error
No suitable WebGL support detected! OmicsNet requires WebGL enabled in your browser. Please click here for possible solutions.
Browser Suggestions
OmicsNet has been developed and tested using Chrome and FireFox, although it also works in the lastest version of Safari and Edge. We suggest you to switch to Chrome browser for best user experience.
Browser Suggestions
The Safari version 10.1 is known to have issues with OmicsNet, we suggest you to upgrade to higher version or switch to Chrome browser or Mozilla Firefox for best user experience.
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