Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development

Schmouth, Jean-François; Arenillas, David; Corso-Díaz, Ximena; Xie, Yuan-Yun; Bohacec, Slavita; Banks, Kathleen G.; Bonaguro, Russell J.; Wong, Siaw H.; Jones, Steven J. M.; Marra, Marco A.; Simpson, Elizabeth M.; Wasserman, Wyeth W.

doi:10.1186/s12864-015-1770-3

Table 2 SOX9 revealed as a candidate co-interactor of Nr2e1 for genes of the “nervous system development”

From: Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development

Transcription factors	No. of background hits	No. of background non-hits	No. of target hits	No. of target non-hits	Z score	Fisher score	ABA Expression at E13.5	ABA Expression at E15.5	ABA Expression at E18.5	Other expression resources	Expression pattern score
SP1	190	310	41	23	20.40	6.53E-05	Not available	Not available	Not available	Ubiquitous^a	++
Nobox	248	252	47	17	17.70	2.13E-04	Weak, Ubiquitous	Moderate, Ubiquitous	Weak	Not applicable	+
SOX9	172	328	40	24	16.97	1.58E-05	Moderate, VZ/SVZ	Moderate, VZ/SVZ	Strong, VZ/SVZ	Not applicable	+++
Arnt-Ahr	243	257	48	16	15.76	4.38E-05	Weak, Ubiquitous	Moderate, Ubiquitous	Moderate, Ubiquitous	Not applicable	++
Nkx2-5	309	191	58	6	15.12	7.92E-07	Not available	Not available	Not available	Absent^b	-
Gfi1	199	301	42	22	14.27	7.74E-05	Not available	Not available	Not available	Strong, ubiquitous^c	++
Lhx3	74	426	20	44	14.00	1.58E-03	Weak	Weak	Weak	Not applicable	+
TAL1-TCF3	93	407	26	38	13.60	1.22E-04	Moderate, Ubiquitous	Moderate, Ubiquitous	Weak, Ubiquitous	Not applicable	+
NHLH1	61	439	22	42	13.57	2.00E-05	Strong, Neocortex	Weak, Neocortex	Weak	Not applicable	++
Myb	211	289	46	18	13.49	5.86E-06	Weak, Neocortex	Weak, Neocortex	Weak	Not applicable	++
Roaz (Zfp423)	59	441	19	45	12.99	3.31E-04	Not available^a	Not available^a	Not available	Strong, ubiquitous^d	++
FOXI1	189	311	36	28	12.27	3.72E-03	Weak	Weak	Weak	Not applicable	+
Prrx2	296	204	53	11	12.26	1.13E-04	Weak	Weak	Weak	Not applicable	+
Cebpa	131	369	37	27	11.92	6.32E-07	Weak	Weak	Weak, Neocortex	Not applicable	+
Foxa2	177	323	35	29	11.38	2.38E-03	Weak, Ubiquitous	Weak, Ubiquitous	Weak, Ubiquitous	Not applicable	+
NFYA	68	432	18	46	11.36	3.60E-03	Moderate, Ubiquitous	Moderate, Ubiquitous	Moderate, Ubiquitous, Neocortex	Not applicable	++
Sox17	237	263	48	16	11.06	2.06E-05	Weak	Weak	Weak	Not applicable	+
Sox5	269	231	51	13	10.61	4.18E-05	Strong, Neocortex	Strong, Neocortex	Strong, Neocortex	Not applicable	++
SRY	267	233	48	16	10.11	6.56E-04	Weak	Weak	Weak	Not applicable	+
MYC-MAX	32	468	12	52	10.07	1.87E-03	Moderate, Ubiquitous	Moderate, Ubiquitous	Moderate, Ubiquitous, Neocortex	Not applicable	++

Bold, most relevant transcription factor according to both the statistical and expression pattern scores; Not available, no expression data available in the ABA (http://www.brain-map.org/, accessed January 10^th 2014); Not applicable, data available in ABA so no need to access other resources
^aGray et al. (PMID: 15618518) showed expression in the central nervous system, including the brain ventricular layers at E13.5
^bExpression restricted to the developing striatum at E14.5 according to Eurexpress (http://www.eurexpress.org/)
^cWallis et al. (PMID: 12441305) showed expression in the developing forebrain at E12.5
^dExpression strong and ubiquitous in the developing brain according to Eurexpress and GenePaint at E14.5 (http://www.genepaint.org/Frameset.html)

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ISSN: 1471-2164

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