A novel network visual analytics system for creating and exploring relationships among
genes, proteins, miRNAs, metabolites or transcription factors
in three-dimensional (3D) space

Click an icon below to start


  • ID types: Entrez, Ensembl Gene/Transcript, Uniprot and official gene symbol
  • Databases: InnateDB, STRING, and IntAct

Transcription factors

  • ID types: Entrez, Ensembl Gene/Transcript, Uniprot and official gene symbol
  • Databases: TRRUST, ENCODE, and JASPAR


  • ID types: miRBase Accession and miRBase ID
  • Databases: miRNet (miRTarbase and TarBase)


  • ID types: KEGG ID, HMDB ID, PubChem and CHEBI ID
  • Databases: KEGG and Recon2

Graph file

  • File formats: .sif, .graphml or .txt (edge list)

Project Objective

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 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 several network toplology analyses to gain systems-level insights.

Please Cite

  • 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/Protein List Upload
Enter your gene/protein list below: help

You can copy and paste your list of significant genes with optional associated p values or fold changes separated by tab. A small example data is shown below (first column: Entrez ID, second column: fold change):

5743	24.25
3552	21.85
6364	14.64
3553	13.07
10148	10.87
6349	9.19
3620	-8.38
50486	-7.25
2919	-6.96
3557	-6.4
629	-6.07
27074	-6.02

miRNA List Upload
Enter your miRNA list below: help
Metabolite List Upload
Enter your metabolites list below: help
Transcription Factor List Upload
Enter your transcription factor list below: help
Upload a Graph File
A small network (.txt)
A large network (.graphml)

Supported file formats: .graphml, .sif or .txt file containing edge list. For more information, please read our FAQs or download example files below.

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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