Table 2.

Functional categories of differentially expressed genes (either upregulated (up) or downregulated (down)) at E11.5 and E12.5 in Fgf9^−/−;Fgf20^−/− versus control mesenchyme.

E11.5 down	Term	PValue	Genes
	PEA3-type ETS-domain transcription factor	3.27E-06	Etv1, Etv5, Etv4
	Nucleus	0.0015755	Hnrnpm, Csrp2bp, Zfp146, Rfc2, Ccnd2, Ebf1, Etv1, Nup85, Etv5, Etv4, Tfdp1, Phlda1
	Transcription factor activity	0.00210736	Zfp146, Ebf1, Etv1, Etv5, Etv4, Tfdp1
	Ubl conjugation	0.00250484	Hnrnpm, Zfp146, Ccnd2, Ebf1, Etv1, Etv5, Etv4
	Cyclins and Cell Cycle Regulation	0.05486549	Ccnd2, Tfdp1
E11.5 up	Collagen binding	0.00900509	Dcn, Sparc
	RNA polymerase II regulatory region sequence-specific DNA binding	0.01718199	Gata2, Foxf1, Lmx1a
	Extracellular matrix binding	0.02930471	Dcn, Sparc
	Extracellular space	0.03133622	Sostdc1, Spint1, Igf1, Dcn, Sparc
	Intrinsic apoptotic signaling pathway	0.03396137	Cdkn1a, Ddit4
	Positive regulation of fibroblast proliferation	0.0445977	Cdkn1a, Igf1
	Negative regulation of angiogenesis	0.05773814	Dcn, Sparc
E12.5 down	PEA3-type ETS-domain transcription factor, N-terminal	1.40E-05	Etv1, Etv5, Etv4
	Developmental protein	0.00421589	Sema5a, Irx3, Spry1, Itga8, Kazald1, Pou3f3, Spry4, Tcf15
	Negative regulation of cell adhesion	0.00447761	Sema5a, Epha5, Tnc
	Regulation of actin cytoskeleton organization	0.00629443	Epha5, Pam, Gpm6b
	Negative regulation of ERK1 and ERK2 cascade	0.01076025	Spry1, Timp3, Spry4
	Chemokine-like protein, FAM19A2	0.01087892	Fam19a1, Fam19a4
	Fibronectin, type III	0.01096813	Epha5, Tnc, Lrrn3, Il13ra1
	Extracellular matrix	0.01348415	Col26a1, Tnc, Kazald1, Timp3
	Sequence-specific DNA binding	0.01910438	Sall3, Irx3, Etv1, Pou3f3, Etv5, Etv4
	Insulin-like growth factor binding protein	0.03280652	Nov, Epha5, Kazald1
E12.5 up	Secreted	2.29E-09	Ccdc80, Igf1, Fam132a, Dcn, Ogn, Bdnf, Cbln2, Gpc3, Serpine2, Srpx2, Penk, Frem1, Sostdc1, Rspo3, Fbln5, Sema3c, Wnt11, Lbp, Col1a1, Col8a1, Prss23, Olfm2
	Extracellular matrix	3.96E-06	Ogn, Fbln5, Frem1, Ccdc80, Wnt11, Col1a1, Dcn, Col8a1
	Developmental protein	7.00E-05	Msx2, Msx1, Meis2, Elf3, Serpine2, Frem1, Sema3c, Tbx1, Wnt11, Zic1, Meis1, Hemgn
	Negative regulation of cell proliferation	1.75E-04	Msx2, Cdkn1a, Msx1, Gpc3, Serpine2, Igf1, Ldoc1, Erdr1
	Positive regulation of transcription, DNA-templated	3.73E-04	Agtr2, Elf3, Foxf1, Igf1, Tbx1, Wnt11, Col1a1, Zic1, Cited4
	Positive regulation of cell migration	0.00359097	Foxf1, Igf1, Sema3c, Wnt11, Col1a1
	Positive regulation of BMP signaling pathway	0.00554745	Msx2, Msx1, Gpc3
	Negative regulation of cell growth	0.00684689	Cdkn1a, Msx1, Serpine2, Wnt11
	Positive regulation of mesenchymal cell apoptotic process	0.00926277	Msx2, Msx1
	Heparin binding	0.01030538	Ogn, Serpine2, Rspo3, Ccdc80
	Inner ear development	0.0178024	Bdnf, Igf1, Lin7a
	Positive regulation of synapse assembly	0.01988632	Bdnf, Cbln2, Srpx2
	Nervous system development	0.02920633	Bdnf, Serpine2, Igf1, Sema3c, Zic1
	Differentiation	0.03351564	Elf3, Serpine2, Sema3c, Cend1, Zic1, Hemgn
	Negative regulation of canonical Wnt signaling pathway	0.03984049	Gpc3, Sostdc1, Wnt11
	Growth factor	0.04868104	Ogn, Bdnf, Igf1