Table 3.

Addition of predicted transcription factors substantially increased connected component

Connected component—without TFS					Connected component with TFS
Module	Genes in fantom	Experimental	Predicted		Experimental	Predicted
Salmon	163	14	47	SP1, NRF2, TCF3, AP1	125	132
Midnight Blue	105	0	14	SP1	75	105
Cyan	150	16	41	SP1, NRF1, SRY, SREBF1, MIR221, MEF2A, TCF3	121	130
Brown	463	31	163	SP1, JUN*, FOXF2, ATF4, TCF3, ELK1, STAT1*, NRF1, MIR132	381	409
Magenta	106	14	26	SP1, ELK1, MEF2A	82	91

For each module, gene symbols were entered into FANTOM4 EdgeExpressDB and a predicted regulatory network was drawn based on experimental evidence (ChIP, published interactions and siRNA experiments), with and without the addition of predicted evidence (predicted transcription factor binding and microRNA). Transcription factors were added based on evidence of significantly over-represented motifs in MSigDB and textual evidence of involvement in Parkinson’s.

^*In the case of the Brown module, STAT1 and JUN were already in the module. “Connected component” consists of all genes that were not singletons in the predicted regulatory network