Extending signalling pathways with protein-interaction networks. Application to apoptosis.

Extending signalling pathways with protein-interaction networks. Application to apoptosis.
Joan Planas-Iglesias, Emre Guney, Javier Garcia-Garcia, Kevin A. Robertson, Sobia Raza, Tom C. Freeman, Peter Ghazal and Baldo Oliva.
OMICS. 2012 May;16(5):245-56. Epub 2012 Mar 2. (PMID: 22385281)

Supplementary materials for "Extending signalling pathways with protein-interaction networks. Application to apoptosis."

Supplementary table 2

Table S2. Number of selected candidates with specific keyword function. Candidates are selected according to the best combination of approaches for each network (experimental, STRING+ and their expansions)*. Second row identifies the functions of the candidates: kinases (K), phosphatases (P), non-phosphor signalling (S) or other functions (O).

Network	Experimental				STRING+				Experimental expansion				STRING+ expansion
Network	Experimental				STRING+				Experimental expansion				a				b
Functions	K	P	S	O	K	P	S	O	K	P	S	O	K	P	S	O	K	P	S	O
Number of candidates	13	3	10	90	48	5	21	155	49	8	19	218	47	5	16	225	63	1	13	194

* *Note: Best combinations are iALD and ALD for Experimental network; ALD, iALD, and FF for STRING+; FF and ALD for Experimental expanded network; and FF, and iALD^a (or SC^b) for STRING+ expanded network (iALD when using KeyWord validation, shown in columns a, and SC when using ProMiner validation, in b)