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Table 3 Cardiac septal defect candidate gene prioritization.

From: Disease candidate gene identification and prioritization using protein interaction networks

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*
  1. 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).