3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics

BMC Bioinformatics

Table 1 Interactions reconstructed by 3off2 and alternative methods for a subnetwork of hematopoiesis regulation. → indicates a successfully recovered interaction including its direction as reported in the literature (see References). $⇏$ corresponds to a successfully recovered interaction, however, with an opposite direction as reported in the literature. ⌿ stipulates that no direct regulatory interaction has been inferred, while — corresponds to an undirected link. Note in particular that Aracne does not infer edge direction. See Additional file 1: Table S1 for supplementary statistics

11 known Regulatory		3off2	PC	PC	MMHC	MMHC	Bayes hc	Bayes hc	Aracne
interactions	References	NML	α = 10 ⁻¹	α = 10 ⁻²	BDe	BIC	BDe	BIC	ε=0
Gata2 → Gfi1b	[36]	→	$⇏$	—	⌿	⌿	→	⌿	⌿
Gfi1 → Gata2	[36]	→	→	—	→	$⇏$	→	$⇏$	—
Gfi1b $⇆$ Gfi1	[36]	$⇏$	$⇏$	—	$⇏$	$⇏$	$⇏$	$⇏$	—
Gfi1 → PU.1	[37]	→	→	⌿	⌿	⌿	→	→	—
Lyl1 → Gfi1	[38]	→	$⇏$	⌿	⌿	⌿	→	$⇏$	—
Ldb1 → Meis1	[39]	→	⌿	⌿	⌿	⌿	$⇏$	⌿	⌿
Ldb1 → Lyl1	[39]	→	⌿	⌿	⌿	⌿	⌿	⌿	⌿
Erg → Lyl1	[40]	→	$⇏$	—	→	→	→	$⇏$	—
Gata2 → Scl	[40]	$⇏$	→	—	→	→	→	→	—
Gfi1b → Meis1	[41]	$⇏$	$⇏$	—	→	→	→	→	—
Gata1 → Gata2	[42]	$⇏$	$⇏$	—	→	→	→	→	—
Correct edges (out of 11)	(→/ $⇏$ /—)	11	9	7	6	6	10	8	8
- Correct orientations	(→)	7	3	0	5	4	8	4	0
- Mis/non-orientations	( $⇏$ / —)	4	6	7	1	2	2	4	8
Missing links	(⌿)	0	2	4	5	5	1	3	3

ISSN: 1471-2105