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I have downloaded parts of them to the graphics server, listed as follows:

Data in use

1. bo graph

This network shows yeast protein interactions. Proteins can have direct or indirect interactions with one another. Indirect interaction refers to being a member of the same functional module (e.g., transcription initiation complex, ribosome) but without directly binding to one another. In contrast, direct interaction refers to two amino acid chains that binds to each other. Obviously, many of these interactions reflect the dynamic state of the cell and are present or absent depending on the particular environment or developmental status of the cell. However, the sum of existing and potential interactions altogether defines the protein network and is ultimately encoded within the genome of a given organism.

The network consists of one big cluster and several isolated clusters. The largest cluster, which is the graph used here, contains 1458 out of 1870 proteins (~78%).

Interesting notes from the nature paper "Lethality and centrality in protein networks":
"Due to its size, a complete map of the network (Fig. 1a), while informative, in itself offers little insight into its large-scale characteristics."
"This indicates that the network of protein interactions in two separate organisms forms a highly inhomogeneous scale-free network in which a few highly connected proteins play a central role in mediating interactions among numerous, less connected proteins."


2. hep-th graph

It is a weighted network of coauthorships between scientists posting preprints on the High-Energy Theory E-Print Archive between Jan 1, 1995 and December 31, 1999.


3. as-rel.20071008 graph

It is the autonomous systems graph on Oct. 8th 2007, and it is obtained from CAIDA. The original graph is directed, we converted it to undirected graph by ignoring the direction.

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