Example Data Sets

These data sets have been generously contributed by users. Please feel free to add your own.

Annotated Human Interactome

A new human interactome dataset has been generated, merging molecular interaction data from a variety of sources. Of key importance is that the new datasets contain information about how interactions were identified, and IDs to link back to source databases and pubmed articles. Further details are given in the readme file:




Human interactome Readme file

Readme file

15 May 2007

Human interactome SIF file

sif file

15 May 2007

Zipped up human interactome and tab delimited annotation files

zip file

15 May 2007

Any questions or comments should be sent to:

Andrew dot Garrow at Unilever dot com

Human Interactome Data

Two recent pieces of work have increased the coverage of the "Human Interactome" by using high-throughput yeast two-hybrid systems to systematically test pairwise interactions between human genes.

In recent work we wrote a simple programme to parse the data from these studies (available as supplementary material on the publication websites) and created .sif and .na files to allow the visualisation and analysis of these interaction networks using Cytoscape.

The interaction files are based on different types of evidence including the interactions measured with the Y2H system plus mass-spec based validation and interactions from literature curation. The node annotation files contain the HUGO IDs that correspond to the EntrezGeneIDs. I will post README files for these interaction datasets in the near future, but in the meantime browsing the interactions file will give a good impression of the interaction data they contain.


Interaction File

Interaction Types

Node Attributes

Rual et al
Nature. 2005 Oct 20;437(7062):1173-8


interaction measured by HTP Y2H system
GST Pull down assay result used to test for false +ve rate
core, non-core, hypercore:
Literature-based interactions


Stelzl et al
Cell. 2005 Sep 23;122(6):957-68


High-confidence Y2H interaction
Low-confidence Y2H interaction
Supporting evidence of interaction reported in literature
GST_PullDown, coAP_Assay:
Supporting Mass-Spec data


If you have any questions or comments please get in touch on:

guy dot warner at unilever dot com

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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