The network was clustered into groups of genes sharing similar profiles using the MCL algorithm with an empirical MCL inflation value (1.8) and a global graph for each network was created showing the MCL clusters.
In short, the MCL value is an average of the percentage C labelling in a given metabolite.
For the identification of tandem duplicates, we first classified gene family using the software MCL with E value < 1E-10, and then defined tandem duplicates as follows: 1) belonging to the same gene family, 2) being located within 5 kb each other, and 3) being separated by ≤ 3 non-homologous genes.
To compute the sizes of protein families, the 109,595 proteins of the 10 fungal genomes were clustered into gene families based on sequence similarities (BLASTP; e-value < 1e−6) using the TRIBE-MCL algorithm (Additional file 10: Table S7; [ 72]).
The participants completed the perceived ease of use and perceived usefulness questionnaires after using the GPS-based MCL system.
When creating complex estimates from Collins et al. (2007), we used MCL with the same parameters as described above, and used the PE values as the input to the MCL algorithm.
The clusters are then extracted from the network using the Markov clustering (MCL) algorithm (18).
Sequences were clustered using the Markov cluster (MCL) algorithm [ 54] with default parameters (Additional file 4).
However, unlike other groups [20], we did not detect Mcl-1 caspase-cleavage products in our control samples using the same anti-Mcl-1 antibody.
The graph comprised 24,808 nodes connected by 1,476,632 edges and was subsequently clustered using the Markov clustering algorithm (MCL) at an inflation value (which controls the granularity of clustering) of 2.2.
OrthoMCL clustering analyses were performed using the following parameters: p-value cut-off = 1 × 10−5; Percent Identity cut-off = 0; Percent match cut-off = 80; MCL Inflation = 1.5; Maximum weight = 316.
