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).

Chen et al. BMC Bioinformatics 2009 10:73   doi:10.1186/1471-2105-10-73

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