Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare

BMC Systems Biology

Table 1 Quantitative changes of blood interactomes during developmental transitions

	Protein interaction networks		PPICompare results
Transition	Interactome sizes n_i→n_j	Δn_i→n_j	P_rew	obs_s/obs_all	rew₊/rew₋	rew₊−rew₋
HSC →MPP	101,235 ± 30,315→111,556 ± 10,069	10,321 ± 31,944	0.372	15/18 (0.83)	311/123	188 (0.32 σ)
MPP →CMP	111,556 ± 10,069→117,254 ± 3176	5698 ± 10,558	0.278	9/9 (1.00)	856/423	433 (0.50 σ)
MPP →CLP	111,556 ± 10,069→79,383 ± 31,849	–32,173 ± 33,402	0.455	15/15 (1.00)	1/705	–704 (0.94 σ)
CMP →MEP	117,254 ± 3176→117,768 ± 8692	513 ± 9254	0.261	8/12 (0.67)	3955/2532	1423 (0.10 σ)
CMP →GMP	117,254 ± 3176→121,051 ± 6427	3796 ± 7169	0.256	6/9 (0.67)	8468/5556	2912 (0.12 σ)
MEP →EB	117,768 ± 8692→111,326 ± 28,549	–6441 ± 29,842	0.348	20/28 (0.71)	3021/4146	–1125 (0.18 σ)
MEP →MK	117,768 ± 8692→132,598 ± 8456	14,831 ± 12,126	0.293	12/20 (0.60)	10,574/3848	6726 (0.67 σ)
GMP →N	121,051 ± 6427→67,007 ± 9203	–54,044 ± 11,225	0.585	24/30 (0.80)	3895/41,599	–37,704 (1.46 σ)
GMP →M	121,051 ± 6427→113,534 ± 2762	–7517 ± 6995	0.337	10/15 (0.67)	15,763/21,407	–5644 (0.27 σ)
CLP →CD4	79,383 ± 31,849→120,282 ± 19,498	40,898 ± 37,343	0.512	30/40 (0.75)	17,181/1919	15,262 (0.69 σ)

The net change in number of interactions Δ n _i→n _j is reported as the mean difference between all samples per cell type and its standard deviation. obs_s is the minimum number of rewired obervations out of all pairwise comparisons obs_all that were necessary for a rewiring event to be called significant in PPICompare applied to that transition. For increased comparability, the fraction as a floating-point number is given in brackets. The number of rewiring events deemed significant by PPICompare is depicted as rew₊ for emerging interactions and rew_- for vanishing interactions. In addition to the net change among significant rewiring events, its absolute deviation to Δ n _i→n _j in terms of standard deviations σ(Δ n _i→n _j) is shown in brackets

ISSN: 1752-0509