R Graphics Output

Gene Set 1630 : AXON_GUIDANCE Gene Set Null Distribution Heat Map for Genes in Gene Set G1[B_Ph] G2[Non_B_Ph] Class ABL1 GNAI1 FYN ABLIM1 NRP1 EFNA1 RHOA PLXNB2 Gene Set Null Density SEMA6A ITGB1 NCK1 EPHA4 5 Observed Gene Set ES value RGS3

0.2 PPP3CA NFATC1 SLIT2 EPHA2 EFNB3 RAC2 SEMA3E RAC3 PAK1 EPHA5 FES RHOD RASA1 EFNA2 SEMA3D

4 DPYSL2 PAK4 0.0 SRGAP2 SEMA4D LIMK1 EPHB1 PLXNA1 PLXNC1 PAK7 DCC MET ROCK2 SEMA6B RAC1 PLXNA2 CDC42 UNC5C 3 SEMA5A SEMA7A

−0.2 GSK3B MAPK3 MAPK1 EPHB4 ROBO1

SEMA3C Zero crossing at 6147 CXCL12 RND1 NRAS PPP3CC P(ES) Peak at 1258 PPP3CB L1CAM PAK2 CDK5 EFNB1 2 NTNG1 PAK3 −0.4 SEMA4A GNAI2 SLIT3 SEMA3A PTK2 EPHB3 PPP3R1 NFATC3 EPHB6 NTN1 SEMA4C SEMA6D NCK2 UNC5B Running Enrichment Score (RES)

1 EPHA3 NFAT5

−0.6 GNAI3 SEMA3G ABLIM3 KRAS SEMA3B EPHA7 EFNA5 EPHB2 EPHA1 LIMK2 EFNA4 ROCK1 PLXNA3 SEMA6C SEMA4G 0 CFL1 SEMA3F −0.8 SEMA4F PAK6 ARHGEF12 Neg. ES "G2[Non_B_Ph]" Pos. ES: "G1[B_Ph]" SLIT1 "G1[B_Ph]" "G2[Non_B_Ph]" CXCR4 SRGAP3 NFATC4 EFNB2 PLXNB1

0 2000 4000 6000 8000 10000 12000 −0.4 −0.2 0.0 0.2 0.4 swp350.u133a.CEL JD.ALD388.v5.U133A.CEL JD.ALD428.v5.U133A.CEL JD.ALD494.v5.U133A.CEL JD.ALD035.v5.U133A.CEL JD.ALD039.v5.U133A.CEL JD.ALD391.v5.U133A.CEL JD.ALD264.v5.U133A.CEL JD.ALD386.v5.U133A.CEL JD.ALD387.v5.U133A.CEL JD.ALD389.v5.U133A.CEL JD.ALD390.v5.U133A.CEL JD.ALD008.v5.U133A.CEL JD.ALD613.v5.U133A.CEL JD.ALD509.v5.U133A.CEL JD.ALD096.v5.U133A.CEL JD.ALD108.v5.U133A.CEL JD.ALD057.v5.U133A.CEL JD.ALD232.v5.U133A.CEL JD.ALD294.v5.U133A.CEL JD.ALD385.v5.U133A.CEL JD.ALD052.v5.U133A.CEL JD.ALD078.v5.U133A.CEL JD.ALD433.v5.U133A.CEL JD.ALD180.v5.U133A.CEL JD.ALD009.v5.U133A.CEL JD0154.ALL.v5.U133A.CEL JD0206.ALL.v5.U133A.CEL JD0102.ALL.v5.U133A.CEL JD0129.ALL.v5.U133A.CEL JD0192.ALL.v5.U133A.CEL JD0181.ALL.v5.U133A.CEL JD0239.ALL.v5.U133A.CEL JD0032.ALL.v5.U133A.CEL JD0361.ALL.v5.U133A.CEL JD0336.ALL.v5.U133A.CEL JD0267.ALL.v5.U133A.CEL JD0323.ALL.v5.U133A.CEL JD0150.ALL.v5.U133A.CEL JD0059.ALL.v5.U133A.CEL JD0123.ALL.v5.U133A.CEL JD0056.ALL.v5.U133A.CEL JD0058.ALL.v5.U133A.CEL JD0139.ALL.v5.U133A.CEL JD0107.ALL.v5.U133A.CEL JD0109.ALL.v5.U133A.CEL JD0085.ALL.v5.U133A.CEL JD0253.ALL.v5.U133A.CEL JD0426.ALL.v5.U133A.CEL JD0286.ALL.v5.U133A.CEL JD0282.ALL.v5.U133A.CEL JD0318.ALL.v5.U133A.CEL JD0066.ALL.v5.U133A.CEL JD0016.ALL.v5.U133A.CEL JD0048.ALL.v5.U133A.CEL JD0086.ALL.v5.U133A.CEL JD0193.ALL.v5.U133A.CEL JD0280.ALL.v5.U133A.CEL JD0320.ALL.v5.U133A.CEL JD0330.ALL.v5.U133A.CEL JD0328.ALL.v5.U133A.CEL JD0250.ALL.v5.U133A.CEL JD0220.ALL.v5.U133A.CEL JD0304.ALL.v5.U133A.CEL JD0395.ALL.v5.U133A.CEL JD0341.ALL.v5.U133A.CEL JD0263.ALL.v5.U133A.CEL JD0364.ALL.v5.U133A.CEL JD0437.ALL.v5.U133A.CEL JD0436.ALL.v5.U133A.CEL JD0382.ALL.v5.U133A.CEL JD0354.ALL.v5.U133A.CEL JD0342.ALL.v5.U133A.CEL JD0238.ALL.v5.U133A.CEL JD0247.ALL.v5.U133A.CEL JD0264.ALL.v5.U133A.CEL JD0390.ALL.v5.U133A.CEL JD0423.ALL.v5.U133A.CEL JD0432.ALL.v5.U133A.CEL JD0344.ALL.v5.U133A.CEL JD0039.ALL.v5.U133A.CEL JD0255.ALL.v5.U133A.CEL JD0421.ALL.v5.U133A.CEL JD0408.ALL.v5.U133A.CEL JD0080.ALL.v5.U133A.CEL JD0084.ALL.v5.U133A.CEL JD0124.ALL.v5.U133A.CEL JD0284.ALL.v5.U133A.CEL JD0349.ALL.v5.U133A.CEL JD0396.ALL.v5.U133A.CEL JD0108.ALL.v5.U133A.CEL JD0146.ALL.v5.U133A.CEL JD0360.ALL.v5.U133A.CEL JD0367.ALL.v5.U133A.CEL JD0314.ALL.v5.U133A.CEL JD0420.ALL.v5.U133A.CEL JD0343.ALL.v5.U133A.CEL JD0173.ALL.v5.U133A.CEL JD0258.ALL.v5.U133A.CEL JD0287.ALL.v5.U133A.CEL JD0103.ALL.v5.U133A.CEL JD0425.ALL.v5.U133A.CEL JD0225.ALL.v5.U133A.CEL JD0433.ALL.v5.U133A.CEL JD0431.ALL.v5.U133A.CEL JD0252.ALL.v5.U133A.CEL JD0188.ALL.v5.U133A.CEL JD0272.ALL.v5.U133A.CEL JD0289.ALL.v5.U133A.CEL JD0407.ALL.v5.U133A.CEL JD0257.ALL.v5.U133A.CEL JD0095.ALL.v5.U133A.CEL JD0226.ALL.v5.U133A.CEL JD0260.ALL.v5.U133A.CEL JD0036.ALL.v5.U133A.CEL JD0381.ALL.v5.U133A.CEL JD0203.ALL.v5.U133A.CEL JD0246.ALL.v5.U133A.CEL JD0274.ALL.v5.U133A.CEL JD0334.ALL.v5.U133A.CEL JD0186B.ALL.v5.U133A.CEL JD0185B.ALL.v5.U133A.CEL JD0332.R.ALL.v5.U133A.CEL JD0168.B.ALL.v5.U133A.CEL JD0297.R.ALL.v5.U133A.CEL JD0300.RR.ALL.v5.U133A.CEL JD0291.RR.ALL.v5.U133A.CEL Gene List Index ES Number of genes: 12930 (in list), 106 (in gene set) ES = 0.295 NES = 1.26 Nom. p−val= 0.113 FWER= 1 FDR= 0.485