Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality

Table 2 Seven representative motifs identified by GIMF.

	Pathway or complex	Seed gene	Motif gene list
1	Actin patch assembly	ARC40	ARP2
2	Chitin synthase III pathway	CHS7	CHS3, SKT5, CHS5
		CHS6	CHS3, SKT5
3	Prefoldin complex	PAC10	GIM3, GIM4, GIM5, YKE2
4	Membrane traffic	ARL1	ARL3, RIC1, YPT6
		GYP1	RIC1
5	Dynein Dynactin pathway	DYN1	ARP1, DYN1, PAC11, YMR299C, DYN2, JNM1, PAC1, NIP100, NUM1
		PAC1	ARP1, DYN1, PAC11, YMR299C, DYN2, JNM1, NIP100, NUM1
		JNM1	ARP1, DYN1, PAC11, YMR299C, DYN2, NIP100, NUM1
		NUM1	JNM1
6	DNA replication checkpoint	MRC1	TOF1
7	Sister chromatid cohesion	DCC1	CTF4, CTF18
		CTF8	CTF18, DCC1, CTF4

These gene modules correlate well with pathways inferred by hierarchical clustering (Tong et al. 2004).

ISSN: 1471-2105