Welcome to the web interface of SAMNet, or Simultaneous Analysis of Multiple Networks. This tool should help you analyze multiple gene expression datasets with upstream data. You can select from the examples we've provided below or enter your own files. Please read the tutorial for information on how to format your files.

Source Weights File (e.g. protein/genetic weights)

Upload protein weights (tab-delimited text) file here*:
OR select a test dataset:

Note: Protein node names must be consistent with protein node naming in the interactome or protein-mRNA weights file. To use the interactomes provided, please use UNIPROT entry names or HUGO/HGNC gene names.

Sink Weights File (e.g. mRNA weights)

Upload mRNA weights (tab-delimited text) file here*:
OR select a test dataset:

Protein-protein Interaction File

Upload an interactome here (pickle-compressed NetworkX object or tab-delimited text file):

OR select a database interactome:

Connecting mRNA weights to interactome

Upload protein-mRNA edge weights (pickle-compressed NetworkX object or tab-delimited text) file here*:

OR select a database for TF to DNA interactions:
OR Check here to connect sink weights directly to interactome:
Use sink weights directly

Gamma (Default - 14):
Hierarchical Capacities:
Use hierarchical capacities
Your Email Address:
(optional: for notification of job status)
Your user ID:
(optional: limited to 3 characters)


1. Gosline S.J.C., Oh C., Fraenkel E. (2015) SAMNetWeb: identifying condition-specific networks linking signaling and transcription, Bioinformatics, 31(7): 1124-6.

2. Gosline S.J.C., Spencer S.J., Ursu O., Fraenkel E. (2012) SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets, Integrative Biology, 4:1415-27.


Any questions or issues please contact Sara Gosline at: sgosline _at_ mit _dot_ edu.

This website is free and open to all users and no login required.