Table 3. Transcription factors identified using MatInspector (Cartharius et al., 2005).

Matrix family	p-value∗	Description	GO terms associated with the matrix family
V$ETSF	0.00685405	Human and murine ETS1 factors	Motor neuron axon guidance, neuron fate specification, neuron maturation, peripheral nervous system neuron development, positive regulation of neuron death and differentiation.
V$SORY	0.00970298	SOX/SRY-sex/testis determining and related HMG box factors	Brain development, Central, enteric, sympathetic and peripheral nervous system development, CNS neuron differentiation, myelination in peripheral nervous system, spinal cord development, spinal cord motor neuron differentiation and ventral spinal cord interneuron specification.
V$RXRF	0.0124996	RXR heterodimer binding sites	Brain development, central and peripheral nervous system development, CNS neuron differentiation, CNS projection neuron axonogenesis, dopaminergic and midbrain neuron differentiation, forebrain neuron development, neuron differentiation, migration and maturation, negative regulation of neuron apoptotic process, and positive regulation of neuron differentiation.
V$WHNF	0.0208955	Winged helix binding sites	Neuron fate commitment, ventral spinal cord interneuron fate commitment.
V$HOMF	0.0231715	Homeodomain transcription factors	Brain development, Central and enteric nervous system development, neuron differentiation, neuron migration, negative regulation of neuron apoptotic process and regulation of neuron differentiation.
V$BPTF	0.0255628	Bromodomain and PHD domain transcription factors	Brain development.
V$RP58	0.0257514	RP58 (ZFP238) zinc finger protein	Cerebellum development, cerebral cortex development, hippocampus development and neuron development.
V$FKHD	0.0346126	Fork head domain factors	Brain development and morphogenesis, enteric, sympathetic and peripheral nervous system development, CNS neuron development, myelination in central nervous system, regulation of nervous system development, cell morphogenesis in neuron differentiation, dopaminergic neuron differentiation, motor neuron axon guidance, negative regulation of neuron differentiation, neuron development and differentiation, neuron fate determination and specification, neuron stem cell population maintenance, pyramidal neuron migration, positive regulation of neuron apoptotic process and differentiation, spinal cord development and ventral spinal cord interneuron specification.
V$NKXH	0.0376881	NKX homeodomain factors	Brain development, nervous system development, cerebral cortex, forebrain neuron differentiation, spinal cord motor neuron differentiation, motor neuron axon guidance, forebrain neuron fate commitment, negative regulation of neuron apoptotic process, and positive regulation of neuron differentiation, neuron fate commitment, neuron fate specification, neuron migration, spinal cord oligodendrocyte cell differentiation and fate specification, ventral spinal cord interneuron differentiation and fate determination.
V$IRXF	0.0537914	Iroquois homeobox transcription factors	CNS development, CNS neuron differentiation, negative regulation of neuron differentiation, neuron maturation, positive regulation of neuron differentiation and retinal bipolar neuron differentiation.
V$ATBF	0.06225	AT-binding transcription factor	Brain development, regulation of neuron differentiation.
V$ZICF	0.0637499	Members of ZIC-family, zinc finger protein of the cerebellum	Brain development, cell proliferation in forebrain, midbrain and hindbrain, CNS development, determination of right/left asymmetry in nervous system, forebrain morphogenesis, retinal ganglion cell axon guidance, spinal cord development.
V$ABDB	0.0678214	Abdominal-B type homeodomain transcription factors	Peripheral nervous system neuron development and spinal cord motor neuron cell fate specification.
V$SIXF	0.0726783	Sine oculis (SIX) homeodomain factors	Brain development, peripheral nervous system neuron development, generation of neurons, negative regulation of neuron apoptotic process and neuron differentiation, neuron fate specification.
V$BRNF	0.0784254	Brn POU domain factors	Brain development, CNS neuron differentiation, myelination in peripheral nervous system, peripheral nervous system neuron development and differentiation, forebrain neuron differentiation, neuron development, differentiation, neuron fate commitment and fate specification, neuron projection development and negative regulation of neuron apoptotic process.
V$HOXC	0.0805504	HOX-PBX complexes	Brain development and segmentation, CNS neuron differentiation, peripheral nervous system neuron development and differentiation, motor neuron axon guidance, positive & negative regulation of neuron differentiation, neuron development, differentiation and migration, dorsal spinal cord development and spinal cord motor neuron cell fate specification.
V$HBOX	0.086678	Homeobox transcription factors	Brain development, embryonic brain development, autonomic nervous system development, CNS development and neuron differentiation, cell morphogenesis involved in neuron differentiation, dopaminergic neuron differentiation, forebrain neuron development, motor neuron axon guidance, negative regulation of neuron death and neuron apoptotic process, neuron development, differentiation, death, fate commitment, migration, fate specification and projection morphogenesis, sensory neuron axon guidance, subpallium neuron fate commitment, spinal cord association neuron differentiation, spinal cord neuron cell fate specification, spinal cord motor neuron differentiation and spinal cord interneuron specification.
V$LHXF	0.0890478	Lim homeodomain factors	Brain development, CNS neuron development and differentiation, peripheral nervous system neuron axonogenesis and neuron development, GABAergic and dopaminergic neuron differentiation, forebrain neuron development, differentiation and fate commitment, lateral motor column neuron migration, medial motor column neuron differentiation, midbrain-hindbrain boundary development, motor neuron axon guidance, negative regulation of neuron apoptotic process and differentiation, neuron development, differentiation, fate commitment, fate specification, maturation and migration, positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation, spinal cord development, spinal cord association neuron differentiation, spinal cord motor neuron cell fate specification, spinal cord motor neuron differentiation, ventral spinal cord interneuron specification. and visceral motor neuron differentiation.
V$BRN5	0.0896913	Brn-5 POU domain factors	Brain development, CNS development and ganglion mother cell fate determination.
V$DLXF	0.095084	Distal-less homeodomain transcription factors	Brain and nervous system development, neuron development and differentiation, negative regulation of neuron apoptotic process and regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment.
V$HIFF	0.0956065	Hypoxia inducible factor, bHLH/PAS protein family	Brain development, CNS development, dopaminergic neuron differentiation, motor neuron axon guidance, negative regulation of oxidative-stress induced neuron intrinsic apoptotic signalling pathway and neuron apoptotic process.
V$TALE	0.0960602	TALE homeodomain class recognizing TG motifs	Brain morphogenesis, enteric nervous system development, neural crest cell migration involved in autonomic nervous system development and positive & negative regulation of neuron differentiation.
V$RORA	0.0967563	v-ERB and RAR-related orphan receptor alpha	Brain development.
V$HESF	0.0988147	Vertebrate homologues of enhancer of split complex	Brain development, CNS development, myelination in CNS, peripheral nervous system development, GABAergic neuron differentiation in basal ganglia, cell morphogenesis involved in neuron differentiation, positive & negative regulation of neuron differentiation, negative regulation of neuron projection development, neuron stem cell population maintenance, regulation of neuronal synaptic plasticity and regulation of timing of neuron differentiation.
V$HOXH	0.0995363	HOX-MEIS1 heterodimers	Enteric nervous system development, peripheral nervous system neuron development, neural crest cell migration involved in autonomic nervous system development, negative regulation of neuron differentiation and spinal cord motor neuron cell fate specification.
V$BCDF	0.103333	Bicoid-like homeodomain transcription factors	Brain development, CNS development, dopaminergic neuron differentiation, positive regulation of neuron apoptotic process, neuron development, neuron differentiation, neuron fate commitment, neuron fate determination and neuron proliferation in midbrain.
V$NKX6	0.105076	NK6 homeobox transcription factors	CNS myelination and neuron differentiation, positive regulation of neuron differentiation, regulation of neuron migration, regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification, spinal cord motor neuron differentiation and regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification.
V$NEUR	0.105134	NeuroD, Beta2, HLH domain	Brain development, CNS development, CNS neuron development, enteric nervous system development, peripheral nervous system development, peripheral nervous system neuron development, sympathetic and parasympathetic nervous systems development, commitment of neuronal cell to specific neuron type in forebrain, dopaminergic neuron differentiation, forebrain neuron development and differentiation, generation of neurons, positive & negative regulation of neuron differentiation, noradrenergic neuron differentiation and neuron fate commitment, neuron development, neuron differentiation, neuron fate commitment, neuron fate determination, neuron migration, regulation of timing of subpallium neuron differentiation, spinal cord association neuron differentiation, spinal cord motor neuron cell fate specification, spinal cord motor neuron differentiation, spinal cord oligodendrocyte cell differentiation and fate specification, subpallium neuron fate commitment, sympathetic ganglion development, spinal reflex action, dorsal spinal cord development, spinal cord development, ventral spinal cord interneuron differentiation and fate commitment, vestibulocochlear nerve development and trigeminal nerve development.