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Table 1.

Specific downregulation of TrkA transcripts in Brn3a-null trigeminal ganglia at E13.5

	Experiment 1									Experiment 2
Description	GenBank Accession Number	Wild type	Heterozygote	Knockout	KO×HT change P	Wild type	heterozygote	Knockout	KO×HT change P	Expn
Neurotrophin receptor TrkA	AW124632	2335	2667	1417	0.9999+	n.d.	3252	1528	0.999+	0.54
Housekeeping genes
Creatine kinase, brain	X04591	8716	10366	9254	0.5	5613	6415	8772	0.031	1.16
Cytochrome c oxidase, subunit VIIa3	AF037371	5021	4704	4102	0.5	5228	5303	5409	0.5	0.94
Heat shock protein, 60 kDa, HSP60	X53584	6906	9422	6643	0.5	8075	7540	8458	0.5	0.95
Mitochondrial H+-ATP synthase, subunit g	Y17223	6795	6541	6609	0.5	5524	6680	6601	0.5	1.03
Phosphoglycerate kinase 1	M15668	1864	2147	2155	0.773	2659	2986	2641	0.5	0.99
Ribosomal protein L3	Y00225	6702	8446	7500	0.5	8540	8874	9275	0.294	1.03
Ribosomal protein S3	X76772	9473	11577	9801	0.5	8908	9193	10301	0.5	1.03
Neural genes
BDNF	X55573	240	183	255	0.5	408	327	433	0.095	1.19
Doublecortin	AB011678	4753	5892	6581	0.5	5428	5796	6696	0.5	1.21
Ephreceptor B4	U06834	2255	2283	2218	0.5	2566	2604	2532	0.5	0.98
Ephrin A2	U14941	417	542	532	0.933	466	431	474	0.5	1.08
Microtubule-binding protein tau, probe set 1	M18775	7669	9582	9007	0.5	7994	8485	9590	0.148	1.1
Microtubule-binding protein tau, probe set 2	M18776	5063	5771	4866	0.666	4279	4606	4741	0.5	0.97
Neural cell-adhesion molecule 1 (Ncam 1)	X15052	9356	9637	10969	0.5	7575	8431	9197	0.5	1.15
Opioidreceptor, sigma 1	AF004927	1231	1164	1095	0.5	868	994	925	0.5	0.95
Presenilin I	L42177	1551	1467	1435	0.5	1462	1298	1618	0.5	1.06
Synapsin II	AF096867	764	916	823	0.589	717	738	804	0.5	1.04

	Experiment 1									Experiment 2
Description	GenBank Accession Number	Wild type	Heterozygote	Knockout	KO×HT change P	Wild type	heterozygote	Knockout	KO×HT change P	Expn
Neurotrophin receptor TrkA	AW124632	2335	2667	1417	0.9999+	n.d.	3252	1528	0.999+	0.54
Housekeeping genes
Creatine kinase, brain	X04591	8716	10366	9254	0.5	5613	6415	8772	0.031	1.16
Cytochrome c oxidase, subunit VIIa3	AF037371	5021	4704	4102	0.5	5228	5303	5409	0.5	0.94
Heat shock protein, 60 kDa, HSP60	X53584	6906	9422	6643	0.5	8075	7540	8458	0.5	0.95
Mitochondrial H+-ATP synthase, subunit g	Y17223	6795	6541	6609	0.5	5524	6680	6601	0.5	1.03
Phosphoglycerate kinase 1	M15668	1864	2147	2155	0.773	2659	2986	2641	0.5	0.99
Ribosomal protein L3	Y00225	6702	8446	7500	0.5	8540	8874	9275	0.294	1.03
Ribosomal protein S3	X76772	9473	11577	9801	0.5	8908	9193	10301	0.5	1.03
Neural genes
BDNF	X55573	240	183	255	0.5	408	327	433	0.095	1.19
Doublecortin	AB011678	4753	5892	6581	0.5	5428	5796	6696	0.5	1.21
Ephreceptor B4	U06834	2255	2283	2218	0.5	2566	2604	2532	0.5	0.98
Ephrin A2	U14941	417	542	532	0.933	466	431	474	0.5	1.08
Microtubule-binding protein tau, probe set 1	M18775	7669	9582	9007	0.5	7994	8485	9590	0.148	1.1
Microtubule-binding protein tau, probe set 2	M18776	5063	5771	4866	0.666	4279	4606	4741	0.5	0.97
Neural cell-adhesion molecule 1 (Ncam 1)	X15052	9356	9637	10969	0.5	7575	8431	9197	0.5	1.15
Opioidreceptor, sigma 1	AF004927	1231	1164	1095	0.5	868	994	925	0.5	0.95
Presenilin I	L42177	1551	1467	1435	0.5	1462	1298	1618	0.5	1.06
Synapsin II	AF096867	764	916	823	0.589	717	738	804	0.5	1.04

The values indicate the expression ratio (Expn), which is the average of the knockout values for the two experiments, divided by the average of the wild-type and heterozygote values. The KO × HT change P is the statistical P value of the difference of the target mRNA level between Brn3a knockout and heterozygous animals. Change P≤0.003(incresed in knockout) or ≥0.997 (decreased in knockout) is considered evidence for significant change. 12,422 transcripts were assayed on the u74A chip. Of these, 4125 were positive in all three genotypes in Experiment 1, 321 were changed by these criteria. Of these, only 55 exhibited a greater than twofold change, i.e. a greater change than TrkA. Results were similar for Experiment 2.

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