Sample Data

The sample data explained here, corresponds to the one data of a bacterial evolution experiment in which Escherichia coli K-12 MG1655 was evolved towards high ethanol tolerance. Details on the data are described by Swings et al. can be found clicking here. and are explained in the tutorial.

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

Genome-Wide Interaction Network

E. Coli Interaction Network Data

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

The network file has been compiled from the following sources:

  • 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 15,930 lines divided in 10 predefined interaction-types (header) and the body.

S. cerevisiae Interaction Network Data

The following genome-wide interaction networks are created from:

  • STRING with a threshold of 0.95 can be downloaded here: Get Network
  • A Strict interaction network generated from the CellMap project, the connections selected are formed when genes have a Pearson correlation coefficient >0.35 between their interaction profiles. The file can be downloaded here: Get Network

Mutation Data

E. Coli Mutation Data

The mutation data obtained from the evolution experiment set-up performed by Swings et al can be downloaded here: Get Mutation File

The mutation file contains the genomic information of 16 parallel evolved E. coli

The file has 2,511 lines including the header. keep in mind that there are 16 different conditions, one for each evolved population.

S. cerevisiae Mutation Data

The mutation data obtained from the Jerison et al. 2017 experiments can be downloaded here: Get Mutation File

The mutation file contains the genomic information of 113 populations of S. cerevisiae descended from 35 founders growth in an optimal temperature (OT) environment.

The file has 275 lines including the header.

Gene-Names Mapping File

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 file has 7,815 lines including the header.

S. cerevisiae Gene-Names Mapping File

The S. cerevisiae 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 file has 7,815 lines including the header.