Table 5

Comparison among three different preprocessing techniques when MCODE tool is selected.

Preprocessing Methods

PPI-Network Modification

Protein Complexes

Protein Fraction

P-Value


Actin Cytoskeleton Organization


Detect Defective Cliques (Suggested)

Add 1 PPI

abp1, app1, rvs167, act1, ysc84

4/6

1.93e-05

No Preprocessing

---

abp1, app1, rvs167, act1, yor284w

3/5

8.10e-04

Betweenness Centrality

Remove 3 PPI (2 core PPI)

abp1, rvs167, ysc84, yor284w

2/4

7.1e-05


Bipolar Cellular Bud Site Selection


Detect Defective Cliques (Suggested)

Add 1 PPI

sla2, las17

2/2

5.30e-04

No Preprocessing

---

sla2, las17

2/2

5.30e-04

Betweenness Centrality

Remove 3 PPI (2 core PPI)

---

---

---


Rho Protein Signal Trasduction


Detect Defective Cliques (Suggested)

Add 1 PPI

cla4, gic2, cdc42

3/3

1.76e-06

No Preprocessing

---

cla4, gic2, cdc42

3/3

1.76e-06

Betweenness Centrality

Remove 3 PPI (2 core PPI)

cla4, gic2, cdc42

3/3

1.76e-06


Table reports a comparison among some of the preprocessing tools contained into the knowledge base of the system.The suggested tool allows the system to reach the smallest p-values for all the complexes.

Fiannaca et al. BMC Bioinformatics 2013 14(Suppl 1):S5   doi:10.1186/1471-2105-14-S1-S5

Open Data