OmicsNet

- a network analytics platform for multi-omics integration

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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)

News & Updates

Fixed the issue with background color update (08/07/2020);
Users can now select the original database for miRNA gene target analysis (07/06/2020);
Click the to share interactive results with your collaborators! (05/18/2020);
Added support for the Human Reference Interactome (HuRI) map (05/13/2020);
Updated Java (from Java8 to Java11) and Primefaces (from PF7 to PF8) (04/08/2020);
Fixed the issue with pie chart node disappearing after network customization (03/25/2020);
Added support to upload both genes and proteins in the network and display nodes as pie charts (03/05/2020);
Code cleaning and performance enhancement for Steiner Tree computing (02/05/2020);

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.

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).

Acknowledgement

Gene List Upload

Enter your gene list below:

Specify organism:

Set ID type:

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Genes

KOs

Protein List Upload

Enter your protein list below:

Specify organism:

Set ID type:

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miRNA List Upload

Metabolite List Upload

Transcription Factor List Upload

Upload a Graph File

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.