What types of data does NetworkAnalyst accept?

[Guangyan]

1. NetworkAnalyst currently accepts list(s) of genes or proteins: one or more lists of gene or protein IDs ( from 17 species) with optional expression profiles (i.e. fold changes, p values). Each gene should be in a row. Please refer to our example data for a single list, or multiple lists.

   • Please note when multiple gene/protein lists are uploaded, users will be asked to choose among possible combinations among them for network creation. See an screenshot below (3 lists uploaded)
     
     

2. Network file (any species): users can upload network files generated with a different software to perform network visualization in NetworkAnalyst. Four different formats are supported including .sif, .json, .txt and .graphml format. Please click on the following links to see example files supported:

   • Example .sif format
   • Example .json format from Cytoscape
   • Example .txt format
   • Example .graphml format

NetworkAnalyst is mainly designed for gene/protein lists. We also have three tools for network creation for other purposes:

• OmicsNet: creating general purpose multi-omics network linking all common molecules (including LC-MS peaks and microbiome data!)
• miRNet: creating miRNA-centric network linking miRNAs with genes, TFs, SNPs, etc
• mGWAS-explorer: connecting metabolites, genes, SNPs

[Irene]

I need your advice in using the PPI function of NetworkAnalyst. Is it better to use the entire set of a dataset’s DEGS as a single genelist input? Can we upload separately only the upregulated genes and only the downregulated genes as data input? Thanks.

[Guangyan]

Uploading the whole list or separately as two lists (up and down) are both fine. One option is not better than the other.

[Irene]

Great! Thanks a lot for your prompt response