Protein co-occurrence viever Escherichia coli

For this approach we took Escherichia coli str. K-12 proteins from Uniprot database (data source : Uniprot ) To search the co-occurrence database use gene names from Uniprot site above, e.g. abrB
We provide 3 ways of collapsing:
» Collapsed on species level - Here we analyse gene co-occurrence across all species. All strains that belong to the same species are considered as one entity in the analysis.
» Collapsed on Escherichia strains - Here we analyse gene co-occurrence only across strains that belong to genus Legionella
» Collapsed on species within Escherichia - Here, we analyse gene co-occurrence across all species that belong to genus Escherichia all strains that belong to the same species are considered as one entity in the analysis.

Significance of protein co-occurrence is assessed by Fisher's exact test. Co-occurrence is detected by performing a BLAST search against NCBI database. Hits with E-value below 1e-5 are considered occurrences of homologs