Sample Data

The sample data explained here, corresponds to the one used in the research paper downloadable clicking here. The experimental evolution studied the effect of high ethanol concentration and hence tolerance in the bacterium Escherichia coli K-12 MG1655.

The individual files can be loaded automatically by clicking the Load Sample Data button, or downloaded individually from below.

E. Coli Interaction Network Data

The genome-wide interaction network can be downloaded here: Get Network

The network file has been compiled from different sources as:

  • KEGG: (de)-methylation, (de)-phosphorylation, and metabolic interactions
  • RegulonDB: Protein-DNA, sigma factor binding, sRNA-DNA interactions
  • STRING: Protein-Protein interactions

The final sample network has 22,108 lines divided in 9 predefined interaction-types (header) and the body.

E. Coli Mutation Data

The mutation data obtained from the evolution experiment set-up can be downloaded here: Get Mutation File

The mutation file contains the genomic information of 16 parallel evolved E. coli populations. The alignment and variant calling processes are explained in the reference paper. Similarly, the structure of the file is explained in our documentation

The file has 2,513 lines including the header. keep in mind that there are 16 different conditions, one for each evolved population.

E. Coli Gene-Names Mapping File

The E. coli mapping gene-names file, can be downloaded here: Get Mapping Names File

The file contains the conversion ids from numerical nomenclature, to gene names. The from column matches the ids used in the network file and mutation file, any mismatch will confuse the program throwing an error.

The file has 7,816 lines including the header.