Properties of the Biodegradation Network

Florencio Pazos, Alfonso Valencia, Victor De Lorenzo

Publication

The generation of the network, the analysis carried out, and the results obtained are described in:

Florencio Pazos, Alfonso Valencia & Victor De Lorenzo. (2003).
The organization of the Microbial Biodegradation Network from a Systems-Biology perspective.
EMBO Rep. 4(10):994-999.

Please cite that paper when using the data and/or figures contained in this web page.

Representations of the full network

PNG files: Legend is on the right. Compounds belonging to the Central Metabolism (CM) are at the bottom. The higher a compound is in the figures the longer is its path to the CM.

The PDF files contain easier to follow network layouts generated with DOT (see below). The compounds are not sorted according with any criteria but efficient layout. Central Metabolism (CM) is shown as a node at the bottom. Compound chemical structures are not shown. See the legend in the corresponding PNG files.

Reactions colored by number of organisms where the enzyme is present. ( PNG/ PDF).
Reactions colored by the enzyme 1st EC number. ( PNG/ PDF).
Chemical compounds colored by water solubility. ( PNG/ PDF).
Chemical compounds colored by number of connections. ( PNG/ PDF). Square/higher-res ( JPG 3Mb/ GIF 5Mb). )
Chemical compounds colored by molecular weight. ( PNG/ PDF).
Chemical compounds colored by molecular weight and reactions by enzyme 1st EC number. ( PNG/ PDF).

Network description

The file biodeg_net.dot contains the network description in .DOT format. You can inspect and manipulate it with the DOTTY/DOT or GraphViz programs.

Raw data

The files themselves contain a description of the format.

Florencio Pazos Cabaleiro.
pazos@cnb.csic.es