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)

Further Images for "Extending signalling pathways with protein-interaction networks. Application to apoptosis."

Further Figures showing detailed results from the five-fold cross-validation

The following files contain Sensitivity (black), Specificity (green) and PPV (red) values obtained at certain scoring method threshold on the 5-fold cross-validation analysis.Each file contains several rows and two columns. The columns correspond to the values for Experimental network (left) and STRING+ network (right). The rows correspond to the scoring system analyzed:

Figure Legend	Paper Legend	Meaning
DBs	NoDB	Number of databases describing a particular PPI
Methods	NoM	Number of experimental methods that have elucidated a particular PPI
ALD	ALD	Apoptosis Linking Degree
iALD	iALD	iterative Apoptosis Linking Degree
FF	FF	Functional Flow
SC	SC	STRING combined score
Coexpression	Coexpression	One of the STRING terms that form the STRING combined score. Stands for gene co-expression
Cons. Neighbor	Conserved Neighborhood	One of the STRING terms that form the STRING combined score. Stands for gene conserved neighborhood
Databases	Databases	One of the STRING terms that form the STRING combined score. Stands for imports from manually curated pathway databases
Gene Fusion	Gene Fusion	One of the STRING terms that form the STRING combined score. Stands for gene fusion
HT Experiments	HT Experiments	One of the STRING terms that form the STRING combined score. Stands for information obtained by STRING from published high-throughput protein interaction experiments (yeast two hibrid, tandem affinity purification)
Text Mining	Text Mining	One of the STRING terms that form the STRING combined score. Stands for information obtained by STRING by text mining
P. Co-ocurrance	Phylo. Co-ocurrance	One of the STRING terms that form the STRING combined score. Stands for phylogenetic co-ocurrance

The following table contains links that lead to the mentioned files. Right column contains files for non-expanded networks and left column contains files for orthology expanded networks. The rows indicate which scoring methods contain the files:

Scoring Method	Non expanded	Orthology expanded
NoDB, NoM, ALD, iALD	Further_Figure1_a1	Further_Figure1_b1
FF, SC, Co-expression, Conserved Neighborhood	Further_Figure1_a2	Further_Figure1_b2
Database imports, Gene Fusion, HT Experiments, Text Mining	Further_Figure1_a3	Further_Figure1_b3
Phylogenetic co-ocurrance	Further_Figure1_a4	Further_Figure1_b4