. 2009 Feb 27;10:73. doi: 10.1186/1471-2105-10-73

Table 3.

Cardiac septal defect candidate gene prioritization.

Rank	Integrative functional annotation based ranking (using ToppGene)	PPIN-based ranking (K-Step Markov)	PPIN-based ranking (Hits with Priors)	PPIN-based ranking (PageRank with Priors)
1	TGFBR2*^#	MYL7*	MYL7*	MYL7*

2	EGFR*	PEX19	PEX19	PEX19

3	SMAD4*	NPHP1	NPHP1	NPHP1

4	*SRF**^#	HDAC1*	MAGED1	MAGED1

5	FOS	MAGED1	BMP2*	BMP2*

6	ACVR1B	BMP2*	HDAC1*	HDAC1*

7	*SMAD2**	*SRF**^#	IGBP1	IGBP1

8	ERBB2*^#	IGBP1	MID2	MID2

9	NOTCH2*^#	GRB2*	*SMAD3**	*SMAD3**

10	FN1*	*SMAD3**	*SRF**^#	*SRF**^#

11	BMPR2*^#	EP300*^#	GRB2*	GRB2*

12	NID2	MID2	MYC*	MYC*

13	*SMAD1**	MYC*	HIPK2	HIPK2

14	*SMAD3**	*SMAD2**	FGF2*	FGF2*

15	INSR*^#	CREBBP*^#	*SMAD2**	*SMAD2**

16	HIPK1	*SMAD1**	*SMAD1**	*SMAD1**

17	RRAS	HIPK2	HDAC3	HDAC3

18	RASA1*	TGFB1*	EP300*^#	EP300*^#

19	MEF2C*	FGF2*	CREBBP*^#	CREBBP*^#

20	RAC1*	AR*	TGFB1*	TGFB1*

The cardiac septal defect sub-network was created using known cardiac septal defect genes (from OMIM) and their immediate interactants, and was prioritized using functional annotation and PPIN based methods. Functional annotation based prioritization was done using ToppGene server. The PPIN based rankings were obtained using 3 methods: K step Markov, Hits with Priors, and PageRank with Priors. The highlighted genes are those occurring in all of the prioritized top 20 genes generated using different methodologies. Note that the Hits with Priors and PageRank with Priors gave identical results (see Additional Files 3, 4 and 5 for the list of genes and prioritization results). The genes marked with * are associated with abnormal heart morphology (ToppGene: 15/20; K-Step Markov: 14/20; and Hits with Priors and PageRank with Priors: 13/20) while those marked with # have been reported to be associated with cardiac septal defects (6/20 and 3/20 in ToppGene and PPIN prioritized top 20 candidate genes for cardiac septal defects).