Gene Expression Literature Summary

• Symbol: Irx3
• Name: Iroquois related homeobox 3
• ID: MGI:1197522

151 matching records from 151 references.

Summary by Age and Assay: Numbers in the table indicate the number of results matching the search criteria.

Age	E6.5	E7	E7.5	E8	E8.5	E9	E9.5	E10	E10.5	E11	E11.5	E12	E12.5	E13	E13.5	E14	E14.5	E15	E15.5	E16.5	E17	E17.5	E18.5	E	P
Immunohistochemistry (section)			1	1	1	1	9	2	10		10		3		5		2		3				1	2	5
In situ RNA (section)			2	1	3	2	8		12		7	2	9		9		5		3	2		2	3	5	9
In situ RNA (whole mount)	2	1	5	5	6	3	17	5	17	1	11	1	5		10		4		2					2
In situ reporter (knock in)					1		1	2	1	1			3			1	2		2	2					4
Northern blot									1							1						1		1
Western blot											1
RT-PCR			1		1		6	2	2		4	4	6	2	14		8	2	7	3	1		2		12
cDNA clones					1								1		1		1						1		2

Summary by Gene and Reference: Number indicates the number of results matching the search criteria recorded for each reference.
* Indicates detailed expression data entries available

Irx3  Iroquois related homeobox 3
Results	Reference
7	J:220960 Akiyama R, Kawakami H, Wong J, Oishi I, Nishinakamura R, Kawakami Y, Sall4-Gli3 system in early limb progenitors is essential for the development of limb skeletal elements. Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):5075-80
1	J:156022 Anderson KR, White P, Kaestner KH, Sussel L, Identification of known and novel pancreas genes expressed downstream of Nkx2.2 during development. BMC Dev Biol. 2009;9:65
1	J:112701 Bailey PJ, Klos JM, Andersson E, Karlen M, Kallstrom M, Ponjavic J, Muhr J, Lenhard B, Sandelin A, Ericson J, A global genomic transcriptional code associated with CNS-expressed genes. Exp Cell Res. 2006 Oct 1;312(16):3108-19
3	J:243561 Basta JM, Robbins L, Denner DR, Kolar GR, Rauchman M, A Sall1-NuRD interaction regulates multipotent nephron progenitors and is required for loop of Henle formation. Development. 2017 Sep 01;144(17):3080-3094
1*	J:313619 Bedogni F, Hevner RF, Cell-Type-Specific Gene Expression in Developing Mouse Neocortex: Intermediate Progenitors Implicated in Axon Development. Front Mol Neurosci. 2021;14:686034
1	J:131960 Bell SM, Schreiner CM, Wert SE, Mucenski ML, Scott WJ, Whitsett JA, R-spondin 2 is required for normal laryngeal-tracheal, lung and limb morphogenesis. Development. 2008 Mar;135(6):1049-58
8*	J:45549 Bellefroid EJ, Kobbe A, Gruss P, Pieler T, Gurdon JB, Papalopulu N, Xiro3 encodes a Xenopus homolog of the Drosophila Iroquois genes and functions in neural specification. EMBO J. 1998 Jan 2;17(1):191-203
1	J:62062 Bosse A, Stoykova A, Nieselt-Struwe K, Chowdhury K, Copeland NG, Jenkins NA, Gruss P, Identification of a novel mouse Iroquois homeobox gene, Irx5, and chromosomal localisation of all members of the mouse Iroquois gene family. Dev Dyn. 2000 May;218(1):160-74
17*	J:45683 Bosse A, Zulch A, Becker MB, Torres M, Gomez-Skarmeta JL, Modolell J, Gruss P, Identification of the vertebrate Iroquois homeobox gene family with overlapping expression during early development of the nervous system. Mech Dev. 1997 Dec;69(1-2):169-81
1	J:239777 Boucherat O, Landry-Truchon K, Berube-Simard FA, Houde N, Beuret L, Lezmi G, Foulkes WD, Delacourt C, Charron J, Jeannotte L, Epithelial inactivation of Yy1 abrogates lung branching morphogenesis. Development. 2015 Sep 01;142(17):2981-95
2*	J:271281 Bowles J, Feng CW, Ineson J, Miles K, Spiller CM, Harley VR, Sinclair AH, Koopman P, Retinoic Acid Antagonizes Testis Development in Mice. Cell Rep. 2018 Jul 31;24(5):1330-1341
2	J:67359 Bruneau BG, Bao ZZ, Fatkin D, Xavier-Neto J, Georgakopoulos D, Maguire CT, Berul CI, Kass DA, Kuroski-de Bold ML, de Bold AJ, Conner DA, Rosenthal N, Cepko CL, Seidman CE, Seidman JG, Cardiomyopathy in Irx4-deficient mice is preceded by abnormal ventricular gene expression. Mol Cell Biol. 2001 Mar;21(5):1730-6
4*	J:51411 Bulfone A, Gattuso C, Marchitiello A, Pardini C, Boncinelli E, Borsani G, Banfi S, Ballabio A, The embryonic expression pattern of 40 murine cDNAs homologous to Drosophila mutant genes (Dres): a comparative and topographic approach to predict gene function. Hum Mol Genet. 1998 Dec;7(13):1997-2006
2*	J:178972 Cajal M, Lawson KA, Hill B, Moreau A, Rao J, Ross A, Collignon J, Camus A, Clonal and molecular analysis of the prospective anterior neural boundary in the mouse embryo. Development. 2012 Jan;139(2):423-36
2	J:335822 Capriati M, Hao C, D'Cruz SC, Monfort C, Chevrier C, Warembourg C, Smagulova F, Genome-wide analysis of sex-specific differences in the mother-child PELAGIE cohort exposed to organophosphate metabolites. Sci Rep. 2023 May 17;13(1):8003
2*	J:119269 Caqueret A, Boucher F, Michaud JL, Laminar organization of the early developing anterior hypothalamus. Dev Biol. 2006 Oct 1;298(1):95-106
2	J:322321 Catela C, Chen Y, Weng Y, Wen K, Kratsios P, Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity. Elife. 2022 Mar 22;11:e70766
1	J:304721 Chang SH, Su YC, Chang M, Chen JA, MicroRNAs mediate precise control of spinal interneuron populations to exert delicate sensory-to-motor outputs. Elife. 2021 Mar 31;10:e63768
1	J:224508 Chatterjee M, Guo Q, Weber S, Scholpp S, Li JY, Pax6 regulates the formation of the habenular nuclei by controlling the temporospatial expression of Shh in the diencephalon in vertebrates. BMC Biol. 2014;12:13
1*	J:189715 Chen H, Palmer JS, Thiagarajan RD, Dinger ME, Lesieur E, Chiu H, Schulz A, Spiller C, Grimmond SM, Little MH, Koopman P, Wilhelm D, Identification of novel markers of mouse fetal ovary development. PLoS One. 2012;7(7):e41683
2	J:174745 Chen JA, Huang YP, Mazzoni EO, Tan GC, Zavadil J, Wichterle H, Mir-17-3p controls spinal neural progenitor patterning by regulating Olig2/Irx3 cross-repressive loop. Neuron. 2011 Feb 24;69(4):721-35
1	J:288298 Chen KQ, Tahara N, Anderson A, Kawakami H, Kawakami S, Nishinakamura R, Pandolfi PP, Kawakami Y, Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4. Genetics. 2020 May;215(1):129-141
7*	J:64020 Christoffels VM, Keijser AG, Houweling AC, Clout DE, Moorman AF, Patterning the embryonic heart: identification of five mouse Iroquois homeobox genes in the developing heart. Dev Biol. 2000 Aug 15;224(2):263-74
6*	J:61328 Cohen DR, Cheng CW, Cheng SH, Hui C, Expression of two novel mouse iroquois homeobox genes during neurogenesis. Mech Dev. 2000 Mar 1;91(1-2):317-21
2*	J:177793 Combes AN, Bowles J, Feng CW, Chiu HS, Khoo PL, Jackson A, Little MH, Tam PP, Koopman P, Expression and functional analysis of Dkk1 during early gonadal development. Sex Dev. 2011;5(3):124-30
2*	J:183829 Correa SM, Washburn LL, Kahlon RS, Musson MC, Bouma GJ, Eicher EM, Albrecht KH, Sex reversal in C57BL/6J XY mice caused by increased expression of ovarian genes and insufficient activation of the testis determining pathway. PLoS Genet. 2012 Apr;8(4):e1002569
3	J:131874 Di-Poi N, Zakany J, Duboule D, Distinct Roles and Regulations for Hoxd Genes in Metanephric Kidney Development. PLoS Genet. 2007 Dec 21;3(12):e232
1*	J:153498 Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, SchmidtK, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, et al., A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol. 2011;9(1):e1000582
1	J:174563 Dykes IM, Tempest L, Lee SI, Turner EE, Brn3a and Islet1 act epistatically to regulate the gene expression program of sensory differentiation. J Neurosci. 2011 Jul 6;31(27):9789-99
2*	J:310178 Efimenko E, Padua MB, Manuylov NL, Fox SC, Morse DA, Tevosian SG, The transcription factor GATA4 is required for follicular development and normal ovarian function. Dev Biol. 2013 Sep 1;381(1):144-58
9	J:265538 Fu A, Oberholtzer SM, Bagheri-Fam S, Rastetter RH, Holdreith C, Caceres VL, John SV, Shaw SA, Krentz KJ, Zhang X, Hui CC, Wilhelm D, Jorgensen JS, Dynamic expression patterns of Irx3 and Irx5 during germline nest breakdown and primordial follicle formation promote follicle survival in mouse ovaries. PLoS Genet. 2018 Aug;14(8):e1007488
1*	J:152838 Fu H, Cai J, Clevers H, Fast E, Gray S, Greenberg R, Jain MK, Ma Q, Qiu M, Rowitch DH, Taylor CM, Stiles CD, A genome-wide screen for spatially restricted expression patterns identifies transcription factors that regulate glial development. J Neurosci. 2009 Sep 9;29(36):11399-408
1*	J:74236 Fu H, Qi Y, Tan M, Cai J, Takebayashi H, Nakafuku M, Richardson W, Qiu M, Dual origin of spinal oligodendrocyte progenitors and evidence for the cooperative role of Olig2 and Nkx2.2 in the control of oligodendrocyte differentiation. Development. 2002 Feb;129(3):681-93
2	J:204578 Gaber ZB, Butler SJ, Novitch BG, PLZF regulates fibroblast growth factor responsiveness and maintenance of neural progenitors. PLoS Biol. 2013 Oct;11(10):e1001676
3	J:189007 Gaborit N, Sakuma R, Wylie JN, Kim KH, Zhang SS, Hui CC, Bruneau BG, Cooperative and antagonistic roles for Irx3 and Irx5 in cardiac morphogenesis and postnatal physiology. Development. 2012 Nov;139(21):4007-19
2	J:147382 Genethliou N, Panayiotou E, Panayi H, Orford M, Mean R, Lapathitis G, Malas S, Spatially distinct functions of PAX6 and NKX2.2 during gliogenesis in the ventral spinal cord. Biochem Biophys Res Commun. 2009 Apr 24;382(1):69-73
2	J:355142 Gomez-Del Arco P, Isern J, Jimenez-Carretero D, Lopez-Maderuelo D, Pineiro-Sabaris R, El Abdellaoui-Soussi F, Torroja C, Vera-Pedrosa ML, Grima-Terren M, Benguria A, Simon-Chica A, Queiro-Palou A, Dopazo A, Sanchez-Cabo F, Jalife J, de la Pompa JL, Filgueiras-Rama D, Munoz-Canoves P, Redondo JM, The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development. Nat Commun. 2024 Oct 4;15(1):8602
3*	J:98371 Gotz K, Briscoe J, Ruther U, Homozygous Ft embryos are affected in floor plate maintenance and ventral neural tube patterning. Dev Dyn. 2005 Jun;233(2):623-30
3*	J:91257 Gray PA, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, Tenzen T, Yuk DI, Tsung EF, Cai Z, Alberta JA, Cheng LP, Liu Y, Stenman JM, Valerius MT, Billings N, Kim HA, Greenberg ME, McMahon AP, Rowitch DH, Stiles CD, Ma Q, Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis. Science. 2004 Dec 24;306(5705):2255-2257
1	J:353335 Grego-Bessa J, Gomez-Apinaniz P, Prados B, Gomez MJ, MacGrogan D, de la Pompa JL, Nrg1 Regulates Cardiomyocyte Migration and Cell Cycle in Ventricular Development. Circ Res. 2023 Nov 10;133(11):927-943
3	J:119151 Grego-Bessa J, Luna-Zurita L, del Monte G, Bolos V, Melgar P, Arandilla A, Garratt AN, Zang H, Mukouyama YS, Chen H, Shou W, Ballestar E, Esteller M, Rojas A, Perez-Pomares JM, de la Pompa JL, Notch signaling is essential for ventricular chamber development. Dev Cell. 2007 Mar;12(3):415-29
2	J:191565 Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, Macura K, Blass G, Kellis M, Werber M, Herrmann BG, The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse. Dev Cell. 2013 Jan 28;24(2):206-14
2	J:87048 Gu G, Wells JM, Dombkowski D, Preffer F, Aronow B, Melton DA, Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development. 2004 Jan;131(1):165-79
2*	J:171409 GUDMAP Consortium, GUDMAP: the GenitoUrinary Development Molecular Anatomy Project. www.gudmap.org. 2004;
1	J:278245 Guo Q, Li JYH, Defining developmental diversification of diencephalon neurons through single cell gene expression profiling. Development. 2019 Apr 1;146(12):dev174284
1	J:233374 Hayashi S, Akiyama R, Wong J, Tahara N, Kawakami H, Kawakami Y, Gata6-Dependent GLI3 Repressor Function is Essential in Anterior Limb Progenitor Cells for Proper Limb Development. PLoS Genet. 2016 Jun;12(6):e1006138
1*	J:115165 Hecht J, Seitz V, Urban M, Wagner F, Robinson PN, Stiege A, Dieterich C, Kornak U, Wilkening U, Brieske N, Zwingman C, Kidess A, Stricker S, Mundlos S, Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model. Gene Expr Patterns. 2007 Jan;7(1-2):102-12
1	J:194051 Heliot C, Desgrange A, Buisson I, Prunskaite-Hyyrylainen R, Shan J, Vainio S, Umbhauer M, Cereghini S, HNF1B controls proximal-intermediate nephron segment identity in vertebrates by regulating Notch signalling components and Irx1/2. Development. 2013 Feb;140(4):873-85
2*	J:186535 Herriges JC, Yi L, Hines EA, Harvey JF, Xu G, Gray PA, Ma Q, Sun X, Genome-scale study of transcription factor expression in the branching mouse lung. Dev Dyn. 2012 Sep;241(9):1432-53
16*	J:71423 Houweling AC, Dildrop R, Peters T, Mummenhoff J, Moorman AF, Ruther U, Christoffels VM, Gene and cluster-specific expression of the Iroquois family members during mouse development. Mech Dev. 2001 Sep;107(1-2):169-74
1	J:344559 Hughes CHK, Smith OE, Meinsohn MC, Brunelle M, Gevry N, Murphy BD, Steroidogenic factor 1 (SF-1; Nr5a1) regulates the formation of the ovarian reserve. Proc Natl Acad Sci U S A. 2023 Aug 8;120(32):e2220849120
1	J:184018 Itou J, Kawakami H, Quach T, Osterwalder M, Evans SM, Zeller R, Kawakami Y, Islet1 regulates establishment of the posterior hindlimb field upstream of the Hand2-Shh morphoregulatory gene network in mouse embryos. Development. 2012 May;139(9):1620-9
1	J:128441 Jacob J, Ferri AL, Milton C, Prin F, Pla P, Lin W, Gavalas A, Ang SL, Briscoe J, Transcriptional repression coordinates the temporal switch from motor to serotonergic neurogenesis. Nat Neurosci. 2007 Nov;10(11):1433-9
2	J:232412 Jeon S, Seong RH, Anteroposterior Limb Skeletal Patterning Requires the Bifunctional Action of SWI/SNF Chromatin Remodeling Complex in Hedgehog Pathway. PLoS Genet. 2016 Mar;12(3):e1005915
1	J:299860 Jin L, Chen Y, Crossman DK, Datta A, Vu T, Mobley JA, Basu MK, Scarduzio M, Wang H, Chang C, Datta PK, STRAP regulates alternative splicing fidelity during lineage commitment of mouse embryonic stem cells. Nat Commun. 2020 Nov 23;11(1):5941
13*	J:99530 Jorgensen JS, Gao L, Irx3 is differentially up-regulated in female gonads during sex determination. Gene Expr Patterns. 2005 Aug;5(6):756-62
1	J:239871 Jussila M, Aalto AJ, Sanz Navarro M, Shirokova V, Balic A, Kallonen A, Ohyama T, Groves AK, Mikkola ML, Thesleff I, Suppression of epithelial differentiation by Foxi3 is essential for molar crown patterning. Development. 2015 Nov 15;142(22):3954-63
2	J:173702 Kim B, Kim Y, Cooke PS, Ruther U, Jorgensen JS, The fused toes locus is essential for somatic-germ cell interactions that foster germ cell maturation in developing gonads in mice. Biol Reprod. 2011 May;84(5):1024-32
3*	J:168037 Kim B, Kim Y, Sakuma R, Hui CC, Ruther U, Jorgensen JS, Primordial germ cell proliferation is impaired in Fused Toes mutant embryos. Dev Biol. 2011 Jan 15;349(2):417-26
2	J:250159 Kim KH, Rosen A, Hussein SM, Puviindran V, Korogyi AS, Chiarello C, Nagy A, Hui CC, Backx PH, Irx3 is required for postnatal maturation of the mouse ventricular conduction system. Sci Rep. 2016 Jan 20;6:19197
1	J:221657 Kong JH, Yang L, Dessaud E, Chuang K, Moore DM, Rohatgi R, Briscoe J, Novitch BG, Notch activity modulates the responsiveness of neural progenitors to sonic hedgehog signaling. Dev Cell. 2015 May 26;33(4):373-87
3	J:130851 Lavado A, Lagutin OV, Oliver G, Six3 inactivation causes progressive caudalization and aberrant patterning of the mammalian diencephalon. Development. 2008 Feb;135(3):441-50
2	J:86477 Lebel M, Agarwal P, Cheng CW, Kabir MG, Chan TY, Thanabalasingham V, Zhang X, Cohen DR, Husain M, Cheng SH, Bruneau BG, Hui CC, The Iroquois homeobox gene Irx2 is not essential for normal development of the heart and midbrain-hindbrain boundary in mice. Mol Cell Biol. 2003 Nov;23(22):8216-25
1*	J:119875 Lebel M, Mo R, Shimamura K, Hui CC, Gli2 and Gli3 play distinct roles in the dorsoventral patterning of the mouse hindbrain. Dev Biol. 2007 Feb 1;302(1):345-55
2*	J:226028 Lewandowski JP, Du F, Zhang S, Powell MB, Falkenstein KN, Ji H, Vokes SA, Spatiotemporal regulation of GLI target genes in the mammalian limb bud. Dev Biol. 2015 Oct 1;406(1):92-103
9*	J:213418 Li D, Sakuma R, Vakili NA, Mo R, Puviindran V, Deimling S, Zhang X, Hopyan S, Hui CC, Formation of proximal and anterior limb skeleton requires early function of Irx3 and Irx5 and is negatively regulated by Shh signaling. Dev Cell. 2014 Apr 28;29(2):233-40
1	J:235083 Li J, Miao L, Shieh D, Spiotto E, Li J, Zhou B, Paul A, Schwartz RJ, Firulli AB, Singer HA, Huang G, Wu M, Single-Cell Lineage Tracing Reveals that Oriented Cell Division Contributes to Trabecular Morphogenesis and Regional Specification. Cell Rep. 2016 Apr 5;15(1):158-70
1	J:94180 Lickert H, Takeuchi JK, Von Both I, Walls JR, McAuliffe F, Adamson SL, Henkelman RM, Wrana JL, Rossant J, Bruneau BG, Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature. 2004 Nov 4;432(7013):107-12
1*	J:86839 Liguori GL, Echevarria D, Improta R, Signore M, Adamson E, Martinez S, Persico MG, Anterior neural plate regionalization in cripto null mutant mouse embryos in the absence of node and primitive streak. Dev Biol. 2003 Dec 15;264(2):537-49
4	J:308430 Lopez-Gonzalez L, Alonso A, Garcia-Calero E, de Puelles E, Puelles L, Tangential Intrahypothalamic Migration of the Mouse Ventral Premamillary Nucleus and Fgf8 Signaling. Front Cell Dev Biol. 2021;9:676121
1*	J:75868 Lu QR, Sun T, Zhu Z, Ma N, Garcia M, Stiles CD, Rowitch DH, Common developmental requirement for olig function indicates a motor neuron/oligodendrocyte connection. Cell. 2002 Apr 5;109(1):75-86
3*	J:162220 Magdaleno S, Jensen P, Brumwell CL, Seal A, Lehman K, Asbury A, Cheung T, Cornelius T, Batten DM, Eden C, Norland SM, Rice DS, Dosooye N, Shakya S, Mehta P, Curran T, BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol. 2006 Apr;4(4):e86
2*	J:66591 Mahlapuu M, Ormestad M, Enerback S, Carlsson P, The forkhead transcription factor Foxf1 is required for differentiation of extra-embryonic and lateral plate mesoderm. Development. 2001 Jan;128(2):155-66
3	J:143586 Manuylov NL, Smagulova FO, Leach L, Tevosian SG, Ovarian development in mice requires the GATA4-FOG2 transcription complex. Development. 2008 Nov;135(22):3731-43
1	J:243618 McCracken KW, Aihara E, Martin B, Crawford CM, Broda T, Treguier J, Zhang X, Shannon JM, Montrose MH, Wells JM, Wnt/beta-catenin promotes gastric fundus specification in mice and humans. Nature. 2017 Jan 12;541(7636):182-187
4*	J:163793 McDonald LA, Gerrelli D, Fok Y, Hurst LD, Tickle C, Comparison of Iroquois gene expression in limbs/fins of vertebrate embryos. J Anat. 2010 Jun;216(6):683-91
1	J:354189 Miao L, Lu Y, Nusrat A, Zhao L, Castillo M, Xiao Y, Guo H, Liu Y, Gunaratne P, Schwartz RJ, Burns AR, Kumar A, DiPersio CM, Wu M, beta1 integrins regulate cellular behaviour and cardiomyocyte organization during ventricular wall formation. Cardiovasc Res. 2024 Sep 21;120(11):1279-1294
2	J:66436 Moorman AF, Houweling AC, de Boer PA, Christoffels VM, Sensitive nonradioactive detection of mRNA in tissue sections. Novel application of the whole-mount in situ hybridization protocol. J Histochem Cytochem. 2001 Jan;49(1):1-8
4	J:116182 Morales D, Hatten ME, Molecular markers of neuronal progenitors in the embryonic cerebellar anlage. J Neurosci. 2006 Nov 22;26(47):12226-36
2	J:261627 Mori K, Nakamura H, Kurooka H, Miyachi H, Tamada K, Sugai M, Takumi T, Yokota Y, Id2 determines intestinal identity through repression of the foregut transcription factor, Irx5. Mol Cell Biol. 2018 Feb 20;
1	J:142333 Mukouyama YS, Deneen B, Lukaszewicz A, Novitch BG, Wichterle H, Jessell TM, Anderson DJ, Olig2+ neuroepithelial motoneuron progenitors are not multipotent stem cells in vivo. Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1551-6
1	J:86051 Muller M, Jabs N, Lork DE, Fritzsch B, Sander M, Nkx6.1 controls migration and axon pathfinding of cranial branchio-motoneurons. Development. 2003 Dec;130(23):5815-26
1*	J:71977 Mummenhoff J, Houweling AC, Peters T, Christoffels VM, Ruther U, Expression of Irx6 during mouse morphogenesis. Mech Dev. 2001 May;103(1-2):193-5
1*	J:82193 Murdoch JN, Doudney K, Gerrelli D, Wortham N, Paternotte C, Stanier P, Copp AJ, Genomic organization and embryonic expression of Igsf8, an immunoglobulin superfamily member implicated in development of the nervous system and organ epithelia. Mol Cell Neurosci. 2003 Jan;22(1):62-74
5	J:158526 Naillat F, Prunskaite-Hyyrylainen R, Pietila I, Sormunen R, Jokela T, Shan J, Vainio SJ, Wnt4/5a signalling coordinates cell adhesion and entry into meiosis during presumptive ovarian follicle development. Hum Mol Genet. 2010 Apr 15;19(8):1539-50
2*	J:333713 Narwidina A, Miyazaki A, Iwata K, Kurogoushi R, Sugimoto A, Kudo Y, Kawarabayashi K, Yamakawa Y, Akazawa Y, Kitamura T, Nakagawa H, Yamaguchi-Ueda K, Hasegawa T, Yoshizaki K, Fukumoto S, Yamamoto A, Ishimaru N, Iwasaki T, Iwamoto T, Iroquois homeobox 3 regulates odontoblast proliferation and differentiation mediated by Wnt5a expression. Biochem Biophys Res Commun. 2023 Apr 2;650:47-54
4	J:103817 Nef S, Schaad O, Stallings NR, Cederroth CR, Pitetti JL, Schaer G, Malki S, Dubois-Dauphin M, Boizet-Bonhoure B, Descombes P, Parker KL, Vassalli JD, Gene expression during sex determination reveals a robust female genetic program at the onset of ovarian development. Dev Biol. 2005 Nov 15;287(2):361-77
2	J:309384 Neirijnck Y, Reginensi A, Renkema KY, Massa F, Kozlov VM, Dhib H, Bongers EMHF, Feitz WF, van Eerde AM, Lefebvre V, Knoers NVAM, Tabatabaei M, Schulz H, McNeill H, Schaefer F, Wegner M, Sock E, Schedl A, Sox11 gene disruption causes congenital anomalies of the kidney and urinary tract (CAKUT). Kidney Int. 2018 May;93(5):1142-1153
1*	J:67816 Niederreither K, Vermot J, Messaddeq N, Schuhbaur B, Chambon P, Dolle P, Embryonic retinoic acid synthesis is essential for heart morphogenesis in the mouse. Development. 2001 Apr;128(7):1019-31
1	J:283357 Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D, The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature. 2019 May;569(7756):361-367
2	J:150755 Oh S, Huang X, Liu J, Litingtung Y, Chiang C, Shh and Gli3 activities are required for timely generation of motor neuron progenitors. Dev Biol. 2009 Jul 15;331(2):261-9
1	J:263215 Osterwalder M, Speziale D, Shoukry M, Mohan R, Ivanek R, Kohler M, Beisel C, Wen X, Scales SJ, Christoffels VM, Visel A, Lopez-Rios J, Zeller R, HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. Dev Cell. 2014 Nov 10;31(3):345-357
3	J:213801 Padua MB, Fox SC, Jiang T, Morse DA, Tevosian SG, Simultaneous gene deletion of gata4 and gata6 leads to early disruption of follicular development and germ cell loss in the murine ovary. Biol Reprod. 2014 Jul;91(1):24
1	J:186856 Paschaki M, Lin SC, Wong RL, Finnell RH, Dolle P, Niederreither K, Retinoic acid-dependent signaling pathways and lineage events in the developing mouse spinal cord. PLoS One. 2012;7(3):e32447
2	J:84976 Pattyn A, Vallstedt A, Dias JM, Sander M, Ericson J, Complementary roles for Nkx6 and Nkx2 class proteins in the establishment of motoneuron identity in the hindbrain. Development. 2003 Sep;130(17):4149-59
1	J:80207 Persson M, Stamataki D, te Welscher P, Andersson E, Bose J, Ruther U, Ericson J, Briscoe J, Dorsal-ventral patterning of the spinal cord requires Gli3 transcriptional repressor activity. Genes Dev. 2002 Nov 15;16(22):2865-78
1	J:197599 Pitetti JL, Calvel P, Romero Y, Conne B, Truong V, Papaioannou MD, Schaad O, Docquier M, Herrera PL, Wilhelm D, Nef S, Insulin and IGF1 receptors are essential for XX and XY gonadal differentiation and adrenal development in mice. PLoS Genet. 2013;9(1):e1003160
1*	J:172979 Potter SS, Hartman HA, Kwan KM, Behringer RR, Patterson LT, Laser capture-microarray analysis of Lim1 mutant kidney development. Genesis. 2007 Jul;45(7):432-9
1	J:171448 Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R, Zuniga A, SHH propagates distal limb bud development by enhancing CYP26B1-mediated retinoic acid clearance via AER-FGF signalling. Development. 2011 May;138(10):1913-23
1*	J:326026 Prokopuk L, Jarred EG, Blucher RO, McLaughlin EA, Stringer JM, Western PS, An essential role for Polycomb Repressive Complex 2 in the mouse ovary. Reproduction. 2022 Feb 17;163(3):167-182
1	J:168317 Qin J, Lin Y, Norman RX, Ko HW, Eggenschwiler JT, Intraflagellar transport protein 122 antagonizes Sonic Hedgehog signaling and controls ciliary localization of pathway components. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1456-61
1	J:276877 Qu X, Harmelink C, Baldwin HS, Tie2 regulates endocardial sprouting and myocardial trabeculation. JCI Insight. 2019 May 21;5
2*	J:125316 Reggiani L, Raciti D, Airik R, Kispert A, Brandli AW, The prepattern transcription factor Irx3 directs nephron segment identity. Genes Dev. 2007 Sep 15;21(18):2358-70
1*	J:103820 Reiter JF, Skarnes WC, Tectonic, a novel regulator of the Hedgehog pathway required for both activation and inhibition. Genes Dev. 2006 Jan 1;20(1):22-7
1	J:165741 Rojas A, Schachterle W, Xu SM, Martin F, Black BL, Direct transcriptional regulation of Gata4 during early endoderm specification is controlled by FoxA2 binding to an intronic enhancer. Dev Biol. 2010 Oct 15;346(2):346-55
1	J:178550 Sabharwal P, Lee C, Park S, Rao M, Sockanathan S, GDE2 regulates subtype-specific motor neuron generation through inhibition of Notch signaling. Neuron. 2011 Sep 22;71(6):1058-70
1*	J:235676 Sakakura E, Eiraku M, Takata N, Specification of embryonic stem cell-derived tissues into eye fields by Wnt signaling using rostral diencephalic tissue-inducing culture. Mech Dev. 2016 Aug;141:90-9
2	J:314288 Samal E, Evangelista M, Galang G, Srivastava D, Zhao Y, Vedantham V, Premature MicroRNA-1 Expression Causes Hypoplasia of the Cardiac Ventricular Conduction System. Front Physiol. 2019;10:235
1	J:309382 Sandireddy R, Cibi DM, Gupta P, Singh A, Tee N, Uemura A, Epstein JA, Singh MK, Semaphorin 3E/PlexinD1 signaling is required for cardiac ventricular compaction. JCI Insight. 2019 Aug 22;4(16)
2	J:216471 Sapkota D, Chintala H, Wu F, Fliesler SJ, Hu Z, Mu X, Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development. Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4086-95
1	J:90666 Satoh K, Kasai M, Ishidao T, Tago K, Ohwada S, Hasegawa Y, Senda T, Takada S, Nada S, Nakamura T, Akiyama T, Anteriorization of neural fate by inhibitor of beta-catenin and T cell factor (ICAT), a negative regulator of Wnt signaling. Proc Natl Acad Sci U S A. 2004 May 25;101(21):8017-21
1	J:70697 Scardigli R, Schuurmans C, Gradwohl G, Guillemot F, Crossregulation between Neurogenin2 and Pathways Specifying Neuronal Identity in the Spinal Cord. Neuron. 2001 Aug;31(2):203-17
2	J:239700 Shekhar A, Lin X, Liu FY, Zhang J, Mo H, Bastarache L, Denny JC, Cox NJ, Delmar M, Roden DM, Fishman GI, Park DS, Transcription factor ETV1 is essential for rapid conduction in the heart. J Clin Invest. 2016 Dec 01;126(12):4444-4459
1	J:308861 Shendy NAM, Broadhurst AL, Shoemaker K, Read R, Abell AN, MAP3K4 kinase activity dependent control of mouse gonadal sex determination. Biol Reprod. 2021 Aug 3;105(2):491-502
4*	J:209112 Shimizu H, Kubo A, Uchibe K, Hashimoto M, Yokoyama S, Takada S, Mitsuoka K, Asahara H, The AERO system: a 3D-like approach for recording gene expression patterns in the whole mouse embryo. PLoS One. 2013;8(10):e75754
2	J:98515 Sirbu IO, Gresh L, Barra J, Duester G, Shifting boundaries of retinoic acid activity control hindbrain segmental gene expression. Development. 2005 Jun;132(11):2611-22
4	J:313344 Son JE, Dou Z, Wanggou S, Chan J, Mo R, Li X, Huang X, Kim KH, Michaud JL, Hui CC, Ectopic expression of Irx3 and Irx5 in the paraventricular nucleus of the hypothalamus contributes to defects in Sim1 haploinsufficiency. Sci Adv. 2021 Oct 29;7(44):eabh4503
1	J:152175 Song MR, Sun Y, Bryson A, Gill GN, Evans SM, Pfaff SL, Islet-to-LMO stoichiometries control the function of transcription complexes that specify motor neuron and V2a interneuron identity. Development. 2009 Sep;136(17):2923-32
1	J:350460 Soussi G, Girdziusaite A, Jhanwar S, Palacio V, Notaro M, Sheth R, Zeller R, Zuniga A, TBX3 is essential for establishment of the posterior boundary of anterior genes and upregulation of posterior genes together with HAND2 during the onset of limb bud development. Development. 2024 Jun 1;151(11)
1	J:84301 Stolt CC, Lommes P, Sock E, Chaboissier MC, Schedl A, Wegner M, The Sox9 transcription factor determines glial fate choice in the developing spinal cord. Genes Dev. 2003 Jul 1;17(13):1677-89
1	J:135133 Sugimori M, Nagao M, Bertrand N, Parras CM, Guillemot F, Nakafuku M, Combinatorial actions of patterning and HLH transcription factors in the spatiotemporal control of neurogenesis and gliogenesis in the developing spinal cord. Development. 2007 Apr;134(8):1617-29
1	J:107228 Sun T, Hafler BP, Kaing S, Kitada M, Ligon KL, Widlund HR, Yuk DI, Stiles CD, Rowitch DH, Evidence for motoneuron lineage-specific regulation of Olig2 in the vertebrate neural tube. Dev Biol. 2006 Apr 1;292(1):152-64
1	J:182258 Taher L, Collette NM, Murugesh D, Maxwell E, Ovcharenko I, Loots GG, Global gene expression analysis of murine limb development. PLoS One. 2011;6(12):e28358
2*	J:194960 Tai G, Hohenstein P, Davies JA, FAK-Src signalling is important to renal collecting duct morphogenesis: discovery using a hierarchical screening technique. Biol Open. 2013;2:416-423
3	J:256234 Takata N, Sakakura E, Eiraku M, Kasukawa T, Sasai Y, Self-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism. Nat Commun. 2017 Nov 7;8(1):1339
1	J:231972 Takata N, Sakakura E, Sasai Y, IGF-2/IGF-1R signaling has distinct effects on Sox1, Irx3, and Six3 expressions during ES cell derived-neuroectoderm development in vitro. In Vitro Cell Dev Biol Anim. 2016 May;52(5):607-15
1	J:101739 Takeuchi JK, Mileikovskaia M, Koshiba-Takeuchi K, Heidt AB, Mori AD, Arruda EP, Gertsenstein M, Georges R, Davidson L, Mo R, Hui CC, Henkelman RM, Nemer M, Black BL, Nagy A, Bruneau BG, Tbx20 dose-dependently regulates transcription factor networks required for mouse heart and motoneuron development. Development. 2005 May;132(10):2463-74
1	J:336298 Taliani V, Buonaiuto G, Desideri F, Setti A, Santini T, Galfre S, Schirone L, Mariani D, Frati G, Valenti V, Sciarretta S, Perlas E, Nicoletti C, Musaro A, Ballarino M, The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart. Elife. 2023 Mar 6;12
5*	J:315948 Tamamura Y, Katsube K, Mera H, Itokazu M, Wakitani S, Irx3 and Bmp2 regulate mouse mesenchymal cell chondrogenic differentiation in both a Sox9-dependent and -independent manner. J Cell Physiol. 2017 Dec;232(12):3317-3336
2	J:297065 Tao H, Lambert JP, Yung TM, Zhu M, Hahn NA, Li D, Lau K, Sturgeon K, Puviindran V, Zhang X, Gong W, Chen XX, Anderson G, Garry DJ, Henkelman RM, Sun Y, Iulianella A, Kawakami Y, Gingras AC, Hui CC, Hopyan S, IRX3/5 regulate mitotic chromatid segregation and limb bud shape. Development. 2020 Oct 5;147(19):dev180042
1*	J:306347 Thier MC, Hommerding O, Panten J, Pinna R, Garcia-Gonzalez D, Berger T, Worsdorfer P, Assenov Y, Scognamiglio R, Przybylla A, Kaschutnig P, Becker L, Milsom MD, Jauch A, Utikal J, Herrmann C, Monyer H, Edenhofer F, Trumpp A, Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells. Cell Stem Cell. 2019 Jan 3;24(1):166-182.e13
5*	J:215487 Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JL, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A,Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR, A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron. 2014 Jul 16;83(2):309-23
1	J:71607 Vallstedt A, Muhr J, Pattyn A, Pierani A, Mendelsohn M, Sander M, Jessell TM, Ericson J, Different levels of repressor activity assign redundant and specific roles to Nkx6 genes in motor neuron and interneuron specification. Neuron. 2001 Sep 13;31(5):743-55
1	J:122745 Vierkotten J, Dildrop R, Peters T, Wang B, Ruther U, Ftm is a novel basal body protein of cilia involved in Shh signalling. Development. 2007 Jul;134(14):2569-77
1*	J:122989 Visel A, Thaller C, Eichele G, GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D552-6
1	J:93182 Wang B, Weidenfeld J, Lu MM, Maika S, Kuziel WA, Morrisey EE, Tucker PW, Foxp1 regulates cardiac outflow tract, endocardial cushion morphogenesis and myocyte proliferation and maturation. Development. 2004 Sep;131(18):4477-87
1	J:139698 Wataya T, Ando S, Muguruma K, Ikeda H, Watanabe K, Eiraku M, Kawada M, Takahashi J, Hashimoto N, Sasai Y, Minimization of exogenous signals in ES cell culture induces rostral hypothalamic differentiation. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11796-801
1*	J:190636 Wiese CB, Ireland S, Fleming NL, Yu J, Valerius MT, Georgas K, Chiu HS, Brennan J, Armstrong J, Little MH, McMahon AP, Southard-Smith EM, A genome-wide screen to identify transcription factors expressed in pelvic ganglia of the lower urinary tract. Front Neurosci. 2012;6:130
2*	J:327232 Wu JPH, Yeung J, Rahimi-Balaei M, Wu SR, Zoghbi H, Goldowitz D, The Transcription Factor Pou3f1 Sheds Light on the Development and Molecular Diversity of Glutamatergic Cerebellar Nuclear Neurons in the Mouse. Front Mol Neurosci. 2022;15:921901
1	J:105927 Wu S, Wu Y, Capecchi MR, Motoneurons and oligodendrocytes are sequentially generated from neural stem cells but do not appear to share common lineage-restricted progenitors in vivo. Development. 2006 Feb;133(4):581-90
1	J:156033 Yan Y, Sabharwal P, Rao M, Sockanathan S, The antioxidant enzyme Prdx1 controls neuronal differentiation by thiol-redox-dependent activation of GDE2. Cell. 2009 Sep 18;138(6):1209-21
1	J:290593 Yen YP, Hsieh WF, Tsai YY, Lu YL, Liau ES, Hsu HC, Chen YC, Liu TC, Chang M, Li J, Lin SP, Hung JH, Chen JA, Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. Elife. 2018 Oct 12;7:e38080
4	J:235212 Yeung J, Ha TJ, Swanson DJ, Goldowitz D, A Novel and Multivalent Role of Pax6 in Cerebellar Development. J Neurosci. 2016 Aug 31;36(35):9057-69
4	J:248077 Yokoyama S, Furukawa S, Kitada S, Mori M, Saito T, Kawakami K, Belmonte JCI, Kawakami Y, Ito Y, Sato T, Asahara H, Analysis of transcription factors expressed at the anterior mouse limb bud. PLoS One. 2017;12(5):e0175673
3*	J:156017 Yokoyama S, Ito Y, Ueno-Kudoh H, Shimizu H, Uchibe K, Albini S, Mitsuoka K, Miyaki S, Kiso M, Nagai A, Hikata T, Osada T, Fukuda N, Yamashita S, Harada D, Mezzano V, Kasai M, Puri PL, Hayashizaki Y, Okado H, Hashimoto M, Asahara H, A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev Cell. 2009 Dec;17(6):836-48
3*	J:149990 Yoshimura K, Kitagawa H, Fujiki R, Tanabe M, Takezawa S, Takada I, Yamaoka I, Yonezawa M, Kondo T, Furutani Y, Yagi H, Yoshinaga S, Masuda T, Fukuda T, Yamamoto Y, Ebihara K, Li DY, Matsuoka R, Takeuchi JK, Matsumoto T, Kato S, Distinct function of 2 chromatin remodeling complexes that share a common subunit, Williams syndrome transcription factor (WSTF). Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9280-5
1	J:143585 Yu W, McDonnell K, Taketo MM, Bai CB, Wnt signaling determines ventral spinal cord cell fates in a time-dependent manner. Development. 2008 Nov;135(22):3687-96
7	J:175992 Zhang SS, Kim KH, Rosen A, Smyth JW, Sakuma R, Delgado-Olguin P, Davis M, Chi NC, Puviindran V, Gaborit N, Sukonnik T, Wylie JN, Brand-Arzamendi K, Farman GP, Kim J, Rose RA, Marsden PA, Zhu Y, Zhou YQ, Miquerol L, Henkelman RM, Stainier DY, Shaw RM, HuiCC, Bruneau BG, Backx PH, Iroquois homeobox gene 3 establishes fast conduction in the cardiac His-Purkinje network. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13576-81
3	J:206589 Zhao C, Guo H, Li J, Myint T, Pittman W, Yang L, Zhong W, Schwartz RJ, Schwarz JJ, Singer HA, Tallquist MD, Wu M, Numb family proteins are essential for cardiac morphogenesis and progenitor differentiation. Development. 2014 Jan;141(2):281-95
1	J:109778 Zhou CJ, Pinson KI, Pleasure SJ, Severe defects in dorsal thalamic development in low-density lipoprotein receptor-related protein-6 mutants. J Neurosci. 2004 Sep 1;24(35):7632-9
1	J:213417 Zhulyn O, Li D, Deimling S, Vakili NA, Mo R, Puviindran V, Chen MH, Chuang PT, Hopyan S, Hui CC, A switch from low to high Shh activity regulates establishment of limb progenitors and signaling centers. Dev Cell. 2014 Apr 28;29(2):241-9