Table 3 Parameter settings for MCL, MRF and MCODE.
From: Identifying protein complexes directly from high-throughput TAP data with Markov random fields
Dataset | MCL | MCL with interaction prob. [9] | MRF | MCODE |
|---|---|---|---|---|
Gavin02 | From [24] | Inflation = 1.8 | ψ = 3.5 | From [24] |
Spoke model | Inflation = 1.8 | ν = 0.346 | Maximum likelihood | Node score percentage = 0.0 |
φ = 1.07 × 10-3 | Complex fluff = 0.2 | |||
ρ = 1.88 × 10-3 | Depth = 100 | |||
Gavin06 | Inflation = 3.0 | Inflation = 3.0 | ψ = 3.5 | From [24] |
Spoke model | ν = 0.407 | Maximum likelihood | Node score percentage = 0.0 | |
φ = 1.35 × 10-3 | Complex fluff = 0.2 | |||
ρ = 3.89 × 10-3 | Depth = 100 | |||
Gavin06 | - | - | ψ = 10.0 | - |
Matrix model | Maximum likelihood |