Table 2

Summary of EWS-FLI1 network analysis

Prediction

Product

Deduction type

Functional type

Source of the prediction


Protein nodes


(PIK3C.) = +

Forward

Type III

obs. mRNA (PIK3C.), pred. (.RAS), pred. IGF1

(.RAS) = +

Backward

Type III

pred. IGFBP3, obs. mRNA IGFBP3

(RAC.) = -

Group of proteins

Backward

Type I

obs. mRNA (RHO.) and obs. cell migration

(TGFB.) = +

Forward

Type III

obs. mRNA TGFB

(TNF.) = +

Forward

Type III

obs. mRNA TGFB


RB1_p = -

Phosphorylated protein

Forward

Type II

pred. PRKCB1


CDC2 = -

Forward

Type II

pred. (((CCNA.)_p):CDC2), pred. (CCNB1 p:CDC2)

ECM1 = +

Forward

Type III

obs. mRNA ECM1

ECM2 = +

Forward

Type III

obs. mRNA ECM2

FASLG = +

Forward

Type III

obs. mRNA FASLG

IER3 = +

Forward

Type III

obs. mRNA IER3

IGF1 = +

Backward

Type I

obs. mRNA ACT1

IGF2 = -

Backward

Type II

obs. mRNA CDKN1C, pred. TP73

IGFBP3 = -

Proteins

Backward

Type I

pred. IGF1, obs. mRNA IGF1

JUN = +

Backward

Type III

obs. mRNA FASLG

MYCBP = -

Forward

Type III

obs. mRNA MYCBP

PRKCB1 = -

Forward

Type III

obs. mRNA PRKCB1

RASA1 = +

Forward

Type III

obs. mRNA RASA1

SKP2 = +

Forward

Type III

obs. mRNA SKP2

TGFBR2 = +

Forward

Type II

pred. mRNA TGFBR2

TNFAIP3 = +

Forward

Type III

obs. mRNA TNFAIP3

TP73 = -

Backward

Type II

obs. mRNA PDGFRB


mRNA and protein complex nodes


mRNA_BCL2 = +

Forward

-

pred. IGFBP3

mRNA_IGF2 = -

mRNAs

Backward

-

pred. IGF2, pred. IGFBP3

mRNA_TGFBR2 = +

Forward

-

obs. EWS-FLI1

mRNA_TP53 = -

Forward

-

pred. JUN


((CCNA.):CDK2) = -

Backward

-

obs. cell-cycle G2

((CCNA.)_p:CDC2) = -

Forward

-

obs. cell-cyle M

((CCNA.)_p:CDK2) = -

Protein complexes

Forward

-

obs. cell-cycle M

(CCNB1:CDC2) = -

Backward

-

obs. cell-cycle M

(CCNB1_p:CDC2) = -

Forward

-

obs. cell-clycle anaphase


List of predictions deduced from EWS-FLI1 regulatory network. 'Deduction' corresponds to the direction of propagation of the regulation in the network. The first part of the table corresponds to functional predictions about proteins. The 'Functional type' column shows the result of the post-processing classification of these predictions detailed in the Method section. The second part of the table gathers relevant predictions about other nodes in the network, that is mRNA and protein-complexes. Although they do allow discussing the dogma of a correlation between mRNA and protein levels, such predictions are used in the Results section to discuss the relevance of predictions about proteins. For each prediction we indicate the source of prediction, which is the minimal set of nodes (observed or predicted) that is needed for the deduction of the prediction. For instance, the first line reads as follows: the prediction about (PIK3C.) protein node is a forward deduction from three sources: the observation on (PIK3C.) mRNA and the predictions about (.RAS) and IGF1 nodes.

Baumuratova et al. BMC Systems Biology 2010 4:146   doi:10.1186/1752-0509-4-146

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