What are the data formats accepted by OmicsNet?

[Guangyan]

1. Lists of molecular IDs or names: The format is such that the first column takes the input type and the second column takes the expression value or any other quantitative measurement. Multiple ID types are supported for different organisms.

   • A list of 691 DE genes from helminth infection signature (download)
   • Data from multi-omics (transcriptomics, metabolomics) study to identify biomarker of intrahepatic cholangiocarcinoma cancer (ICC)
     • List of gene symbols (download)
     • List of metabolites (download)
   • Data from multi-omics (proteomics, metabolomics, microbial taxa) study on inflammatory bowel disaese (IBD).
     • List of proteins (download)
     • List of metabolites (download)
     • List of microbial taxa (download)

2. LC-MS Peak List: OmicsNet accepts MS peaks from LC-MS based untargeted metabolomics studies (formatted as csv or txt). The data list consists of four columns (m/z, RT, intensity and P value, sequentially). The first three columns are mandatory, while P values column is optional. If no p value provided, all annotated compounds will be included for network construction.

   • Example of four columns
   • Example of three columns

3. Network Files: 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