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Genes/Proteins

  • ID types: Entrez, Ensembl Gene/Transcript, Uniprot and official gene symbol

Transcription factors

  • ID types: Entrez, Ensembl Gene/Transcript, Uniprot and official gene symbol

miRNAs

  • ID types: miRBase Accession and miRBase ID

Metabolites

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

Microbiome

  • ID types: KEGG Orthology (KO)

Graph file

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

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).
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

To obtain this file, please go to MetaboAnalyst's Peaks to Pathways module. Performing Mummichog or GSEA for pathway activitiy prediction, then go to the Download page. Locate and download the metaboanalyst_peaks.json file
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
KO List Upload
Enter your KO list below: help
Upload a Graph File
help
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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