Table 2.

InfereCLaDR Top-Ranking Predictions and Their Precision Values

A
RAP1		GCN4		SFP1		MSN2		SOK2		YAP1		HSF1		RPN4		ABF1		TEC1
SEC14	0.67	LYS1	0.85	RPS24A	0.98	YDR391C	0.71	YRO2	0.67	GAC1	0.48	OPI10	0.81	RPN12	0.93	YER010C	0.31	TRX2	0.26
YEL1	0.62	HOM2	0.84	RPL18B	0.92	CMK2	0.64	UIP4	0.67	TAH18	0.46	GGA1	0.66	RPT2	0.92	COA3	0.28	CRH1	0.25
PMT4	0.54	BAT1	0.82	RPS16A	0.92	YLR257W	0.43	YNL194C	0.61	ISF1	0.44	RTC3	0.64	PRE10	0.92	GET2	0.24	YOL019W	0.23
FEN1	0.52	HIS2	0.82	RPL8A	0.90	STF2	0.38	GAD1	0.60	YNR034W-A	0.25	YRO2	0.62	RPT5	0.92	BSD2	0.23	RAX2	0.20
ALG7	0.50	STR2	0.80	RPS18B	0.91	RCN2	0.32	JIP4	0.59	MBR1	0.22	APJ1	0.61	RPN7	0.88	YAH1	0.22	YOL014W	0.18
RBD2	0.44	SDT1	0.76	RPS18A	0.90	HAL5	0.25	MSC1	0.59	MRK1	0.20	LSB1	0.57	RPN1	0.85	TDA5	0.22	TGL2	0.16
RPL18B	0.43	RIB3	0.75	RPL40B	0.90	OXR1	0.24	TFS1	0.56	TCB2	0.18	YGR127W	0.53	RPN10	0.83	MIM1	0.22	YPS3	0.15
RPL16B	0.41	PSF2	0.75	RPL42B	0.88	PNC1	0.24	YNL195C	0.56	GAT2	0.18	YGR250C	0.51	PRE7	0.82	YDR541C	0.18	PHM8	0.14
YLR412C-A	0.40	POS5	0.74	RPS22A	0.88	DOA1	0.23	YJR096W	0.54	YLR460C	0.16	CUR1	0.51	YBR062C	0.81	MGR2	0.18	YBL111C	0.12
HXK2	0.40	SRY1	0.74	RPL9A	0.88	MRP8	0.22	OM45	0.49	ATR1	0.16	SAF1	0.45	PUP1	0.81	SLC1	0.17	RIB4	0.11
B
MGA2M		MOT3M		INO2M		MSN4M		FKH2M		FLO8M		RTG3M		STP1M		LEU3M		NRG1M
PLB2	0.83	FIG2	0.49	HNM1	0.84	YHR022C	0.47	AIM20	0.83	FLO9	0.33	IDH2	0.71	VHR2	0.33	OAC1	0.74	PDE2	0.60
TDA4	0.71	PRM1	0.48	SAH1	0.81	CRS5	0.37	HOF1	0.84	TIR4	0.24	PDH1	0.30	MET17	0.33	BAT1	0.72	PRM7	0.40
YLR413W	0.66	SAG1	0.46	FAS1	0.81	JLP1	0.22	ALK1	0.82	DED81	0.17	AAT2	0.27	MET3	0.32	FRS2	0.66	VTS1	0.28
ALE1	0.65	TIR1	0.46	SAM2	0.78	SNO4	0.20	CLB1	0.81	PAU7	0.15	CPR4	0.22	SUL1	0.30	ILV5	0.52	YLR407W	0.27
FAS1	0.50	PAU24	0.39	CHO1	0.75	FRE7	0.16	YMR030W-A	0.79	MSC7	0.15	ARP3	0.14	MET10	0.28	LEU1	0.49	GFD2	0.26
HEM13	0.46	AAC3	0.39	EPT1	0.67	PUG1	0.13	BUD4	0.78	PAU5	0.14	WTM1	0.14	MET5	0.27	SSB1	0.43	YGR079W	0.24
SUR2	0.36	TIR4	0.35	ADO1	0.63	YEL073C	0.13	CDC5	0.77	ERG24	0.14	IDP1	0.13	MEP2	0.27	MAE1	0.33	YNL095C	0.21
NEM1	0.35	EUG1	0.31	OPI3	0.63	PDC6	0.12	YMR001C-A	0.76	PAU24	0.14	URA8	0.12	PET8	0.21	PAB1	0.26	TRM5	0.20
PEX31	0.35	TIR2	0.27	EHT 1	0.59	GCY1	0.11	KIN3	0.75	NCP1	0.13	ADE3	0.10	GNP1	0.21	YPL260W	0.25	PHO90	0.19
FHN1	0.35	FIG1	0.26	YIP3	0.55	FMP48	0.11	HST3	0.67	YGL108C	0.13	SLP1	0.10	DAL80	0.18	ILV1	0.22	MCH5	0.16

(A) New targets (i.e., interactions not in the Gold Standard) of the ten transcription factors (top row) that are most connected in the Gold Standard. The table also lists the precision values of these interactions, with darker green denoting higher precision.

(B) New targets of ten TFs of medium connectivity. Precision values are calculated using the entire matrix of prediction confidence scores, containing 5,716 genes and 557 TFs. The list of true positives was defined by the Gold Standard. Bold targets correspond to interactions that were not found in any of the four orthogonal datasets listed in Table S1; i.e., these regulatory interactions are entirely new. See Table S3 and Data S1 for more details.