Gene Expression Literature Summary

• Symbol: Hoxd13
• Name: homeobox D13
• ID: MGI:96205

248 matching records from 248 references.

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

Age	E1	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	E19.5	E	P
Immunohistochemistry (section)												1		3							1				1
In situ RNA (section)		1		2		3	1	4		6		11	1	14	1	5	2	5	3		4	2			8
Immunohistochemistry (whole mount)							1			2		2													1
In situ RNA (whole mount)		1	1	3	7	11	7	75	25	86	15	62	5	17	2	2	1	1						14
In situ reporter (knock in)										1		2		1										2
Northern blot																									1
Western blot										2		4		2
RT-PCR	1			1	1	6		7	2	8	2	8	1	5		3	2	1	4	2	1	3	1		7
cDNA clones														1

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

Hoxd13  homeobox D13   (Synonyms: Hox-4.8, spdh)
Results	Reference
1*	J:236309 Aires R, Jurberg AD, Leal F, Novoa A, Cohn MJ, Mallo M, Oct4 Is a Key Regulator of Vertebrate Trunk Length Diversity. Dev Cell. 2016 Aug 8;38(3):262-74
1*	J:68216 Akasaka T, van Lohuizen M, van der Lugt N, Mizutani-Koseki Y, Kanno M, Taniguchi M, Vidal M, Alkema M, Berns A, Koseki H, Mice doubly deficient for the Polycomb Group genes Mel18 and Bmi1 reveal synergy and requirement for maintenance but not initiation of Hox gene expression. Development. 2001 May;128(9):1587-97
1	J:79879 Akiyama H, Chaboissier MC, Martin JF, Schedl A, De Crombrugghe B, The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6. Genes Dev. 2002 Nov 1;16(21):2813-28
1	J:121946 Akiyama H, Stadler HS, Martin JF, Ishii TM, Beachy PA, Nakamura T, de Crombrugghe B, Misexpression of Sox9 in mouse limb bud mesenchyme induces polydactyly and rescues hypodactyly mice. Matrix Biol. 2007 May;26(4):224-33
2	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
2	J:93587 Albrecht AN, Kornak U, Boddrich A, Suring K, Robinson PN, Stiege AC, Lurz R, Stricker S, Wanker EE, Mundlos S, A molecular pathogenesis for transcription factor associated poly-alanine tract expansions. Hum Mol Genet. 2004 Oct 15;13(20):2351-9
9*	J:75699 Albrecht AN, Schwabe GC, Stricker S, Boddrich A, Wanker EE, Mundlos S, The synpolydactyly homolog (spdh) mutation in the mouse -- a defect in patterning and growth of limb cartilage elements. Mech Dev. 2002 Mar;112(1-2):53-67
1*	J:181888 Ashe A, Butterfield NC, Town L, Courtney AD, Cooper AN, Ferguson C, Barry R, Olsson F, Liem KF Jr, Parton RG, Wainwright BJ, Anderson KV, Whitelaw E, Wicking C, Mutations in mouse Ift144 model the craniofacial, limb and rib defects in skeletal ciliopathies. Hum Mol Genet. 2012 Apr 15;21(8):1808-23
1*	J:135300 Babbs C, Furniss D, Morriss-Kay GM, Wilkie AO, Polydactyly in the mouse mutant Doublefoot involves altered Gli3 processing and is caused by a large deletion in cis to Indian hedgehog. Mech Dev. 2008 May-Jun;125(5-6):517-26
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
1	J:175541 Bangs F, Antonio N, Thongnuek P, Welten M, Davey MG, Briscoe J, Tickle C, Generation of mice with functional inactivation of talpid3, a gene first identified in chicken. Development. 2011 Aug;138(15):3261-72
2	J:62547 Barna M, Hawe N, Niswander L, Pandolfi PP, Plzf regulates limb and axial skeletal patterning. Nat Genet. 2000 Jun;25(2):166-72
6	J:283343 Bastida MF, Perez-Gomez R, Trofka A, Zhu J, Rada-Iglesias A, Sheth R, Stadler HS, Mackem S, Ros MA, The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):1090-1096
3*	J:309510 Beccari L, Jaquier G, Lopez-Delisle L, Rodriguez-Carballo E, Mascrez B, Gitto S, Woltering J, Duboule D, Dbx2 regulation in limbs suggests interTAD sharing of enhancers. Dev Dyn. 2021 Sep;250(9):1280-1299
2	J:231885 Beccari L, Yakushiji-Kaminatsui N, Woltering JM, Necsulea A, Lonfat N, Rodriguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D, A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev. 2016 May 15;30(10):1172-86
2*	J:49264 Beckers J, Duboule D, Genetic analysis of a conserved sequence in the HoxD complex: regulatory redundancy or limitations of the transgenic approach?. Dev Dyn. 1998 Sep;213(1):1-11
1	J:58674 Bell SM, Schreiner CM, Scott WJ, Disrupting the establishment of polarizing activity by teratogen exposure. Mech Dev. 1999 Nov;88(2):147-57
1	J:144933 Benazet JD, Bischofberger M, Tiecke E, Goncalves A, Martin JF, Zuniga A, Naef F, Zeller R, A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning. Science. 2009 Feb 20;323(5917):1050-3
1	J:223863 Bhattaram P, Penzo-Mendez A, Kato K, Bandyopadhyay K, Gadi A, Taketo MM, Lefebvre V, SOXC proteins amplify canonical WNT signaling to secure nonchondrocytic fates in skeletogenesis. J Cell Biol. 2014 Dec 8;207(5):657-71
1	J:203823 Billings SE, Pierzchalski K, Butler Tjaden NE, Pang XY, Trainor PA, Kane MA, Moise AR, The retinaldehyde reductase DHRS3 is essential for preventing the formation of excess retinoic acid during embryonic development. FASEB J. 2013 Dec;27(12):4877-89
2*	J:168038 Bimonte S, De Angelis A, Quagliata L, Giusti F, Tammaro R, Dallai R, Ascenzi MG, Diez-Roux G, Franco B, Ofd1 is required in limb bud patterning and endochondral bone development. Dev Biol. 2011 Jan 15;349(2):179-91
1	J:104869 Blanc I, Bach A, Robert B, Unusual pattern of Sonic hedgehog expression in the polydactylous mouse mutant Hemimelic extra-toes. Int J Dev Biol. 2002;46(7):969-74
1	J:200262 Bobick BE, Cobb J, Shox2 regulates progression through chondrogenesis in the mouse proximal limb. J Cell Sci. 2012 Dec 15;125(Pt 24):6071-83
2	J:326458 Bolt CC, Lopez-Delisle L, Hintermann A, Mascrez B, Rauseo A, Andrey G, Duboule D, Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun. 2022 Jun 17;13(1):3488
5	J:308920 Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D, Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun. 2021 Aug 18;12(1):5013
3	J:232486 Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N, Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar;12(3):e1005738
3*	J:78766 Boulet AM, Capecchi MR, Duplication of the Hoxd11 gene causes alterations in the axial and appendicular skeleton of the mouse. Dev Biol. 2002 Sep 1;249(1):96-107
6*	J:71694 Bruneau S, Johnson KR, Yamamoto M, Kuroiwa A, Duboule D, The mouse hoxd13(spdh) mutation, a polyalanine expansion similar to human type ii synpolydactyly (spd), disrupts the function but not the expression of other hoxd genes. Dev Biol. 2001 Sep 15;237(2):345-53
1	J:48000 Brunet LJ, McMahon JA, McMahon AP, Harland RM, Noggin, cartilage morphogenesis, and joint formation in the mammalian skeleton [see comments]. Science. 1998 May 29;280(5368):1455-7
2*	J:36526 Bueno D, Skinner J, Abud H, Heath JK, Double in situ hybridization on mouse embryos for detection of overlapping regions of gene expression. Trends Genet. 1996 Oct;12(10):385-7
2*	J:39658 Buscher D, Bosse B, Heymer J, Ruther U, Evidence for genetic control of Sonic hedgehog by Gli3 in mouse limb development. Mech Dev. 1997 Mar;62(2):175-82
2	J:153595 Butterfield NC, Metzis V, McGlinn E, Bruce SJ, Wainwright BJ, Wicking C, Patched 1 is a crucial determinant of asymmetry and digit number in the vertebrate limb. Development. 2009 Oct;136(20):3515-24
1	J:148411 Cameron DA, Pennimpede T, Petkovich M, Tulp3 is a critical repressor of mouse hedgehog signaling. Dev Dyn. 2009 May;238(5):1140-9
5*	J:274320 Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J, The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019 Feb;566(7745):496-502
1*	J:199480 Cao T, Wang C, Yang M, Wu C, Wang B, Mouse limbs expressing only the Gli3 repressor resemble those of Sonic hedgehog mutants. Dev Biol. 2013 Jul 15;379(2):221-8
2	J:109528 Capellini TD, Di Giacomo G, Salsi V, Brendolan A, Ferretti E, Srivastava D, Zappavigna V, Selleri L, Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression. Development. 2006 Jun;133(11):2263-73
1*	J:232146 Carlson HL, Quinn JJ, Yang YW, Thornburg CK, Chang HY, Stadler HS, LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. PLoS Genet. 2015 Dec;11(12):e1005680
2	J:98432 Chen Y, Knezevic V, Ervin V, Hutson R, Ward Y, Mackem S, Direct interaction with Hoxd proteins reverses Gli3-repressor function to promote digit formation downstream of Shh. Development. 2004 May;131(10):2339-47
1	J:342014 Chen Y, Zhou T, Liao Z, Gao W, Wu J, Zhang S, Li Y, Liu H, Zhou H, Xu C, Su P, Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf. Cell Death Differ. 2023 Oct;30(10):2293-2308
3*	J:71186 Chiang C, Litingtung Y, Harris MP, Simandl BK, Li Y, Beachy PA, Fallon JF, Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev Biol. 2001 Aug 15;236(2):421-35
4*	J:119560 Choi MY, Romer AI, Hu M, Lepourcelet M, Mechoor A, Yesilaltay A, Krieger M, Gray PA, Shivdasani RA, A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development. Development. 2006 Oct;133(20):4119-29
2*	J:98919 Cobb J, Duboule D, Comparative analysis of genes downstream of the Hoxd cluster in developing digits and external genitalia. Development. 2005 Jul;132(13):3055-67
3*	J:153164 Cocquempot O, Brault V, Babinet C, Herault Y, Fork stalling and template switching as a mechanism for polyalanine tract expansion affecting the DYC mutant of HOXD13, a new murine model of synpolydactyly. Genetics. 2009 Sep;183(1):23-30
1*	J:203431 Collette NM, Yee CS, Murugesh D, Sebastian A, Taher L, Gale NW, Economides AN, Harland RM, Loots GG, Sost and its paralog Sostdc1 coordinate digit number in a Gli3-dependent manner. Dev Biol. 2013 Nov 1;383(1):90-105
1	J:213642 Cooper KL, Sears KE, Uygur A, Maier J, Baczkowski KS, Brosnahan M, Antczak D, Skidmore JA, Tabin CJ, Patterning and post-patterning modes of evolutionary digit loss in mammals. Nature. 2014 Jul 3;511(7507):41-5
1	J:143544 Cortellino S, Wang C, Wang B, Bassi MR, Caretti E, Champeval D, Calmont A, Jarnik M, Burch J, Zaret KS, Larue L, Bellacosa A, Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4. Dev Biol. 2009 Jan 1;325(1):225-37
1*	J:49808 Crackower MA, Motoyama J, Tsui LC, Defect in the maintenance of the apical ectodermal ridge in the Dactylaplasia mouse. Dev Biol. 1998 Sep 1;201(1):78-89
5	J:277177 Darbellay F, Bochaton C, Lopez-Delisle L, Mascrez B, Tschopp P, Delpretti S, Zakany J, Duboule D, The constrained architecture of mammalian Hox gene clusters. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13424-13433
1*	J:264204 Deimling SJ, Lau K, Hui CC, Hopyan S, Genetic interaction between Gli3 and Ezh2 during limb pattern formation. Mech Dev. 2018 Jun;151:30-36
1	J:132122 Delgado I, Dominguez-Frutos E, Schimmang T, Ros MA, The incomplete inactivation of Fgf8 in the limb ectoderm affects the morphogenesis of the anterior autopod through BMP-mediated cell death. Dev Dyn. 2008 Mar;237(3):649-58
4	J:203785 Delpretti S, Montavon T, Leleu M, Joye E, Tzika A, Milinkovitch M, Duboule D, Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep. 2013 Oct 17;5(1):137-50
2*	J:181619 Delpretti S, Zakany J, Duboule D, A function for all posterior Hoxd genes during digit development?. Dev Dyn. 2012 Apr;241(4):792-802
1	J:108241 Desai J, Shannon ME, Johnson MD, Ruff DW, Hughes LA, Kerley MK, Carpenter DA, Johnson DK, Rinchik EM, Culiat CT, Nell1-deficient mice have reduced expression of extracellular matrix proteins causing cranial and vertebral defects. Hum Mol Genet. 2006 Apr 15;15(8):1329-41
4	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
3*	J:15507 Dolle P, Dierich A, LeMeur M, Schimmang T, Schuhbaur B, Chambon P, Duboule D, Disruption of the Hoxd-13 gene induces localized heterochrony leading to mice with neotenic limbs. Cell. 1993 Nov 5;75(3):431-41
9*	J:22839 Dolle P, Fraulob V, Duboule D, Developmental expression of the mouse Evx-2 gene: relationship with the evolution of the HOM/Hox complex. Dev Suppl. 1994;:143-53
8*	J:1778 Dolle P, Izpisua-Belmonte JC, Boncinelli E, Duboule D, The Hox-4.8 gene is localized at the 5' extremity of the Hox-4 complex and is expressed in the most posterior parts of the body during development. Mech Dev. 1991 Dec;36(1-2):3-13
8	J:37004 Dolle P, Izpisua-Belmonte JC, Brown JM, Tickle C, Duboule D, HOX-4 genes and the morphogenesis of mammalian genitalia. Genes Dev. 1991 Oct;5(10):1767-7
2*	J:54066 Dupe V, Ghyselinck NB, Thomazy V, Nagy L, Davies PJA, Chambon P, Mark M, Essential roles of retinoic acid signaling in interdigital apoptosis and control of BMP-7 expression in mouse autopods. Dev Biol. 1999 Apr 1;208(1):30-43
2	J:232111 Emechebe U, Kumar P P, Rozenberg JM, Moore B, Firment A, Mirshahi T, Moon AM, T-box3 is a ciliary protein and regulates stability of the Gli3 transcription factor to control digit number. Elife. 2016;5:e07897
1	J:152551 Endoh-Yamagami S, Evangelista M, Wilson D, Wen X, Theunissen JW, Phamluong K, Davis M, Scales SJ, Solloway MJ, de Sauvage FJ, Peterson AS, The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during development. Curr Biol. 2009 Aug 11;19(15):1320-6
1	J:218159 Eshkar-Oren I, Krief S, Ferrara N, Elliott AM, Zelzer E, Vascular patterning regulates interdigital cell death by a ROS-mediated mechanism. Development. 2015 Feb 15;142(4):672-80
1*	J:128903 Feng W, Huang J, Zhang J, Williams T, Identification and analysis of a conserved Tcfap2a intronic enhancer element required for expression in facial and limb bud mesenchyme. Mol Cell Biol. 2008 Jan;28(1):315-25
1	J:106035 Ferrante MI, Zullo A, Barra A, Bimonte S, Messaddeq N, Studer M, Dolle P, Franco B, Oral-facial-digital type I protein is required for primary cilia formation and left-right axis specification. Nat Genet. 2006 Jan;38(1):112-7
2	J:159210 Galli A, Robay D, Osterwalder M, Bao X, Benazet JD, Tariq M, Paro R, Mackem S, Zeller R, Distinct roles of Hand2 in initiating polarity and posterior Shh expression during the onset of mouse limb bud development. PLoS Genet. 2010;6(4):e1000901
1	J:291490 Garriock RJ, Chalamalasetty RB, Zhu J, Kennedy MW, Kumar A, Mackem S, Yamaguchi TP, A dorsal-ventral gradient of Wnt3a/beta-catenin signals controls mouse hindgut extension and colon formation. Development. 2020 Apr 12;147(8):dev185108
4*	J:172775 Gildea DE, Luetkemeier ES, Bao X, Loftus SK, Mackem S, Yang Y, Pavan WJ, Biesecker LG, The pleiotropic mouse phenotype extra-toes spotting is caused by translation initiation factor Eif3c mutations and is associated with disrupted sonic hedgehog signaling. FASEB J. 2011 May;25(5):1596-605
1	J:122568 Gonzalez F, Duboule D, Spitz F, Transgenic analysis of Hoxd gene regulation during digit development. Dev Biol. 2007 Jun 15;306(2):847-59
2	J:214984 Gonzalez-Martin MC, Mallo M, Ros MA, Long bone development requires a threshold of Hox function. Dev Biol. 2014 Aug 15;392(2):454-65
2*	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
5*	J:149067 Grier DG, Thompson A, Lappin TR, Halliday HL, Quantification of Hox and Surfactant Protein-B Transcription during Murine Lung Development. Neonatology. 2009 Feb 10;96(1):50-60
5*	J:171409 GUDMAP Consortium, GUDMAP: the GenitoUrinary Development Molecular Anatomy Project. www.gudmap.org. 2004;
1	J:78767 Guha U, Gomes W, Kobayashi T, Pestell R, Kessler J, In Vivo Evidence That BMP Signaling Is Necessary for Apoptosis in the Mouse Limb. Dev Biol. 2002 Sep 1;249(1):108
1*	J:72303 Haraguchi R, Mo R, Hui C, Motoyama J, Makino S, Shiroishi T, Gaffield W, Yamada G, Unique functions of Sonic hedgehog signaling during external genitalia development. Development. 2001 Nov;128(21):4241-50
1	J:62029 Haraguchi R, Suzuki K, Murakami R, Sakai M, Kamikawa M, Kengaku M, Sekine K, Kawano H, Kato S, Ueno N, Yamada G, Molecular analysis of external genitalia formation: the role of fibroblast growth factor (Fgf) genes during genital tubercle formation. Development. 2000 Jun;127(11):2471-9
1*	J:30345 Haramis AG, Brown JM, Zeller R, The limb deformity mutation disrupts the SHH/FGF-4 feedback loop and regulation of 5' HoxD genes during limb pattern formation. Development. 1995 Dec;121(12):4237-45
2	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:46225 Hayes C, Brown JM, Lyon MF, Morriss-Kay GM, Sonic hedgehog is not required for polarising activity in the Doublefoot mutant mouse limb bud. Development. 1998 Feb;125(3):351-7
1	J:48055 Hecksher-Sorensen J, Hill RE, Lettice L, Double labeling for whole-mount in situ hybridization in mouse. Biotechniques. 1998 Jun;24(6):914-6, 918
1*	J:47900 Herault Y, Beckers J, Kondo T, Fraudeau N, Duboule D, Genetic analysis of a Hoxd-12 regulatory element reveals global versus local modes of controls in the HoxD complex. Development. 1998 May;125(9):1669-77
1*	J:43310 Herault Y, Fraudeau N, Zakany J, Duboule D, Ulnaless (Ul), a regulatory mutation inducing both loss-of-function and gain-of-function of posterior Hoxd genes. Development. 1997 Sep;124(18):3493-500
1*	J:37211 Herault Y, Hraba-Renevey S, van der Hoeven F, Duboule D, Function of the Evx-2 gene in the morphogenesis of vertebrate limbs. EMBO J. 1996 Dec 2;15(23):6727-38
1*	J:154370 Heydeck W, Zeng H, Liu A, Planar cell polarity effector gene Fuzzy regulates cilia formation and Hedgehog signal transduction in mouse. Dev Dyn. 2009 Oct 29;238(12):3035-3042
1	J:58673 Heymer J, Ruther U, Syndactyly of Ft/+ mice correlates with an imbalance in bmp4 and fgf8 expression. Mech Dev. 1999 Nov;88(2):173-81
2	J:308865 Higashijima Y, Nagai N, Yamamoto M, Kitazawa T, Kawamura YK, Taguchi A, Nakada N, Nangaku M, Furukawa T, Aburatani H, Kurihara H, Wada Y, Kanki Y, Lysine demethylase 7a regulates murine anterior-posterior development by modulating the transcription of Hox gene cluster. Commun Biol. 2020 Nov 30;3(1):725
1*	J:149502 Hill P, Gotz K, Ruther U, A SHH-independent regulation of Gli3 is a significant determinant of anteroposterior patterning of the limb bud. Dev Biol. 2009 Apr 15;328(2):506-16
1	J:125087 Hill P, Wang B, Ruther U, The molecular basis of Pallister Hall associated polydactyly. Hum Mol Genet. 2007 Sep 1;16(17):2089-96
4	J:242611 Huang BL, Trofka A, Furusawa A, Norrie JL, Rabinowitz AH, Vokes SA, Mark Taketo M, Zakany J, Mackem S, An interdigit signalling centre instructs coordinate phalanx-joint formation governed by 5'Hoxd-Gli3 antagonism. Nat Commun. 2016 Oct 07;7:12903
1	J:310417 Hwang SH, Somatilaka BN, White K, Mukhopadhyay S, Ciliary and extraciliary Gpr161 pools repress hedgehog signaling in a tissue-specific manner. Elife. 2021 Aug 4;10:e67121
3	J:253972 Hwang SH, White KA, Somatilaka BN, Shelton JM, Richardson JA, Mukhopadhyay S, The G protein-coupled receptor Gpr161 regulates forelimb formation, limb patterning and skeletal morphogenesis in a primary cilium-dependent manner. Development. 2018 Jan 8;145(1):dev154054
1*	J:69781 Ikeya M, Takada S, Wnt-3a is required for somite specification along the anteroposterior axis of the mouse embryo and for regulation of cdx-1 expression. Mech Dev. 2001 May;103(1-2):27-33
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:171052 Itou J, Taniguchi N, Oishi I, Kawakami H, Lotz M, Kawakami Y, HMGB factors are required for posterior digit development through integrating signaling pathway activities. Dev Dyn. 2011 May;240(5):1151-62
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
3	J:312493 Jhanwar S, Malkmus J, Stolte J, Romashkina O, Zuniga A, Zeller R, Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development. Nat Commun. 2021 Sep 28;12(1):5685
1*	J:285195 Kajioka D, Suzuki K, Nakada S, Matsushita S, Miyagawa S, Takeo T, Nakagata N, Yamada G, Bmp4 is an essential growth factor for the initiation of genital tubercle (GT) outgrowth. Congenit Anom (Kyoto). 2020 Jan;60(1):15-21
1	J:162938 Kang X, Qi Y, Zuo Y, Wang Q, Zou Y, Schwartz RJ, Cheng J, Yeh ET, SUMO-specific protease 2 is essential for suppression of polycomb group protein-mediated gene silencing during embryonic development. Mol Cell. 2010 Apr 23;38(2):191-201
2*	J:22469 Kanzler B, Viallet JP, Le Mouellic H, Boncinelli E, Duboule D, Dhouailly D, Differential expression of two different homeobox gene families during mouse tegument morphogenesis. Int J Dev Biol. 1994 Dec;38(4):633-40
1	J:149149 Katsanou V, Milatos S, Yiakouvaki A, Sgantzis N, Kotsoni A, Alexiou M, Harokopos V, Aidinis V, Hemberger M, Kontoyiannis DL, The RNA-binding protein Elavl1/HuR is essential for placental branching morphogenesis and embryonic development. Mol Cell Biol. 2009 May;29(10):2762-76
1*	J:79831 Kawakami T, Kawcak T, Li YJ, Zhang W, Hu Y, Chuang PT, Mouse dispatched mutants fail to distribute hedgehog proteins and are defective in hedgehog signaling. Development. 2002 Dec;129(24):5753-65
1	J:144018 Kawakami Y, Uchiyama Y, Rodriguez Esteban C, Inenaga T, Koyano-Nakagawa N, Kawakami H, Marti M, Kmita M, Monaghan-Nichols P, Nishinakamura R, Izpisua Belmonte JC, Sall genes regulate region-specific morphogenesis in the mouse limb by modulating Hox activities. Development. 2009 Feb;136(4):585-94
11	J:54386 Khoa ND, Hasunuma T, Kobata T, Kato T, Nishioka K, Expression of murine HOXD9 during embryonic joint patterning and in human T lymphotropic virus type I tax transgenic mice with arthropathy resembling rheumatoid arthritis. Arthritis Rheum. 1999 Apr;42(4):686-96
3	J:66264 Kmita M, Kondo T, Duboule D, Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing. Nat Genet. 2000 Dec;26(4):451-4
4	J:59900 Kmita M, van Der Hoeven F, Zakany J, Krumlauf R, Duboule D, Mechanisms of Hox gene colinearity: transposition of the anterior Hoxb1 gene into the posterior HoxD complex. Genes Dev. 2000 Jan 15;14(2):198-211
1*	J:158583 Ko HW, Norman RX, Tran J, Fuller KP, Fukuda M, Eggenschwiler JT, Broad-minded links cell cycle-related kinase to cilia assembly and hedgehog signal transduction. Dev Cell. 2010 Feb 16;18(2):237-47
1	J:36770 Kondo T, Dolle P, Zakany J, Duboule D, Function of posterior HoxD genes in the morphogenesis of the anal sphincter. Development. 1996 Sep;122(9):2651-9
2	J:47366 Kondo T, Zakany J, Duboule D, Control of colinearity in AbdB genes of the mouse HoxD complex. Mol Cell. 1998 Jan;1(2):289-300
1	J:326952 Koyano-Nakagawa N, Gong W, Das S, Theisen JWM, Swanholm TB, Van Ly D, Dsouza N, Singh BN, Kawakami H, Young S, Chen KQ, Kawakami Y, Garry DJ, Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud. Nat Commun. 2022 Jul 21;13(1):4221
1	J:205405 Kozhemyakina E, Ionescu A, Lassar AB, GATA6 is a crucial regulator of Shh in the limb bud. PLoS Genet. 2014 Jan;10(1):e1004072
3*	J:66531 Kraus P, Fraidenraich D, Loomis CA, Some distal limb structures develop in mice lacking Sonic hedgehog signaling. Mech Dev. 2001 Jan;100(1):45-58
2*	J:87042 Krebs O, Schreiner CM, Scott WJ Jr, Bell SM, Robbins DJ, Goetz JA, Alt H, Hawes N, Wolf E, Favor J, Replicated anterior zeugopod (raz): a polydactylous mouse mutant with lowered Shh signaling in the limb bud. Development. 2003 Dec;130(24):6037-47
1*	J:101265 Kuijper S, Feitsma H, Sheth R, Korving J, Reijnen M, Meijlink F, Function and regulation of Alx4 in limb development: complex genetic interactions with Gli3 and Shh. Dev Biol. 2005 Sep 15;285(2):533-44
1	J:338694 Kumar S, Alam SS, Bareke E, Beauchamp MC, Dong Y, Chan W, Majewski J, Jerome-Majewska LA, Sf3b4 regulates chromatin remodeler splicing and Hox expression. Differentiation. 2023 May-Jun;131:59-73
3*	J:205338 Kuss P, Kraft K, Stumm J, Ibrahim D, Vallecillo-Garcia P, Mundlos S, Stricker S, Regulation of cell polarity in the cartilage growth plate and perichondrium of metacarpal elements by HOXD13 and WNT5A. Dev Biol. 2014 Jan 1;385(1):83-93
2	J:144711 Kuss P, Villavicencio-Lorini P, Witte F, Klose J, Albrecht AN, Seemann P, Hecht J, Mundlos S, Mutant Hoxd13 induces extra digits in a mouse model of synpolydactyly directly and by decreasing retinoic acid synthesis. J Clin Invest. 2009 Jan;119(1):146-56
1*	J:150759 Lallemand Y, Bensoussan V, Cloment CS, Robert B, Msx genes are important apoptosis effectors downstream of the Shh/Gli3 pathway in the limb. Dev Biol. 2009 Jul 15;331(2):189-98
1	J:301558 Lee DH, Olson AW, Wang J, Kim WK, Mi J, Zeng H, Le V, Aldahl J, Hiroto A, Wu X, Sun Z, Androgen action in cell fate and communication during prostate development at single-cell resolution. Development. 2021 Jan 11;148(1):dev196048
2	J:66266 Lewandoski M, Sun X, Martin GR, Fgf8 signalling from the AER is essential for normal limb development. Nat Genet. 2000 Dec;26(4):460-3
3*	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
1*	J:293790 Lewis EMA, Sankar S, Tong C, Patterson ES, Waller LE, Gontarz P, Zhang B, Ornitz DM, Kroll KL, Geminin is required for Hox gene regulation to pattern the developing limb. Dev Biol. 2020 Aug 1;464(1):11-23
2	J:69771 Lewis PM, Dunn MP, McMahon JA, Logan M, Martin JF, St-Jacques B, McMahon AP, Cholesterol modification of sonic hedgehog is required for long-range signaling activity and effective modulation of signaling by Ptc1. Cell. 2001 Jun 1;105(5):599-612
2	J:102949 Li C, Xu X, Nelson DK, Williams T, Kuehn MR, Deng CX, FGFR1 function at the earliest stages of mouse limb development plays an indispensable role in subsequent autopod morphogenesis. Development. 2005 Nov;132(21):4755-64
1*	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
2	J:235489 Li J, Wang Q, Cui Y, Yang X, Li Y, Zhang X, Qiu M, Zhang Z, Zhang Z, Suppressor of Fused Is Required for Determining Digit Number and Identity via Gli3/Fgfs/Gremlin. PLoS One. 2015;10(5):e0128006
1	J:109101 Li Y, Zhang H, Litingtung Y, Chiang C, Cholesterol modification restricts the spread of Shh gradient in the limb bud. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6548-53
2	J:223057 Lin C, Yin Y, Bell SM, Veith GM, Chen H, Huh SH, Ornitz DM, Ma L, Delineating a conserved genetic cassette promoting outgrowth of body appendages. PLoS Genet. 2013;9(1):e1003231
1	J:158288 Lin C, Yin Y, Veith GM, Fisher AV, Long F, Ma L, Temporal and spatial dissection of Shh signaling in genital tubercle development. Development. 2009 Dec;136(23):3959-67
2	J:78941 Litingtung Y, Dahn RD, Li Y, Fallon JF, Chiang C, Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity. Nature. 2002 Aug 29;418(6901):979-83
1	J:98800 Liu A, Wang B, Niswander LA, Mouse intraflagellar transport proteins regulate both the activator and repressor functions of Gli transcription factors. Development. 2005 Jul;132(13):3103-11
3	J:79482 Liu Y, Liu C, Yamada Y, Fan CM, growth arrest specific gene 1 acts as a region-specific mediator of the Fgf10/Fgf8 regulatory loop in the limb. Development. 2002 Nov;129(22):5289-300
1*	J:180785 Loebel DA, Hor AC, Bildsoe H, Jones V, Chen YT, Behringer RR, Tam PP, Regionalized Twist1 activity in the forelimb bud drives the morphogenesis of the proximal and preaxial skeleton. Dev Biol. 2012 Feb 15;362(2):132-40
2	J:213641 Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Unal E, Liu J, Floriot S, Barbey S, Gallard Y, Muller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D, Zeller R, Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature. 2014 Jul 3;511(7507):46-51
3	J:184012 Lopez-Rios J, Speziale D, Robay D, Scotti M, Osterwalder M, Nusspaumer G, Galli A, Hollander GA, Kmita M, Zeller R, GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis. Dev Cell. 2012 Apr 17;22(4):837-48
1	J:249936 Lu H, Galeano MCR, Ott E, Kaeslin G, Kausalya PJ, Kramer C, Ortiz-Bruchle N, Hilger N, Metzis V, Hiersche M, Tay SY, Tunningley R, Vij S, Courtney AD, Whittle B, Wuhl E, Vester U, Hartleben B, Neuber S, Frank V, Little MH, Epting D, Papathanasiou P, Perkins AC, Wright GD, Hunziker W, Gee HY, Otto EA, Zerres K, Hildebrandt F, Roy S, Wicking C, Bergmann C, Mutations in DZIP1L, which encodes a ciliary-transition-zone protein, cause autosomal recessive polycystic kidney disease. Nat Genet. 2017 Jul;49(7):1025-1034
4	J:136057 Lu P, Yu Y, Perdue Y, Werb Z, The apical ectodermal ridge is a timer for generating distal limb progenitors. Development. 2008 Apr;135(8):1395-405
1	J:30056 Luo G, Hofmann C, Bronckers AL, Sohocki M, Bradley A, Karsenty G, BMP-7 is an inducer of nephrogenesis, and is also required for eye development and skeletal patterning. Genes Dev. 1995 Nov 15;9(22):2808-20
1*	J:146434 Maatouk DM, Choi KS, Bouldin CM, Harfe BD, In the limb AER Bmp2 and Bmp4 are required for dorsal-ventral patterning and interdigital cell death but not limb outgrowth. Dev Biol. 2009 Mar 15;327(2):516-23
3	J:334725 Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E, A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell. 2023 Apr 10;58(7):565-581.e4
1	J:164551 Matsumoto Y, Matsumoto K, Irie F, Fukushi J, Stallcup WB, Yamaguchi Y, Conditional ablation of the heparan sulfate-synthesizing enzyme Ext1 leads to dysregulation of bone morphogenic protein signaling and severe skeletal defects. J Biol Chem. 2010 Jun 18;285(25):19227-34
1	J:147041 Matsuyama M, Aizawa S, Shimono A, Sfrp controls apicobasal polarity and oriented cell division in developing gut epithelium. PLoS Genet. 2009 Mar;5(3):e1000427
1	J:82850 Monge I, Kondo T, Duboule D, An enhancer-titration effect induces digit-specific regulatory alleles of the HoxD cluster. Dev Biol. 2003 Apr 15;256(2):212-20
3	J:131545 Montavon T, Le Garrec JF, Kerszberg M, Duboule D, Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness. Genes Dev. 2008 Feb 1;22(3):346-59
2	J:178930 Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D, A regulatory archipelago controls hox genes transcription in digits. Cell. 2011 Nov 23;147(5):1132-45
2	J:192248 Montavon T, Thevenet L, Duboule D, Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus. Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20204-11
1	J:211652 Moon H, Song J, Shin JO, Lee H, Kim HK, Eggenschwiller JT, Bok J, Ko HW, Intestinal cell kinase, a protein associated with endocrine-cerebro-osteodysplasia syndrome, is a key regulator of cilia length and Hedgehog signaling. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8541-6
1	J:103158 Moribe H, Takagi T, Kondoh H, Higashi Y, Suppression of polydactyly of the Gli3 mutant (extra toes) by deltaEF1 homozygous mutation. Dev Growth Differ. 2000 Aug;42(4):367-76
1	J:262487 Murgai A, Altmeyer S, Wiegand S, Tylzanowski P, Stricker S, Cooperation of BMP and IHH signaling in interdigital cell fate determination. PLoS One. 2018;13(5):e0197535
2	J:228776 Muto A, Ikeda S, Lopez-Burks ME, Kikuchi Y, Calof AL, Lander AD, Schilling TF, Nipbl and mediator cooperatively regulate gene expression to control limb development. PLoS Genet. 2014 Sep;10(9):e1004671
2	J:247259 Naruse C, Shibata S, Tamura M, Kawaguchi T, Abe K, Sugihara K, Kato T, Nishiuchi T, Wakana S, Ikawa M, Asano M, New insights into the role of Jmjd3 and Utx in axial skeletal formation in mice. FASEB J. 2017 Jun;31(6):2252-2266
3	J:217206 Neufeld SJ, Wang F, Cobb J, Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb. Genetics. 2014 Nov;198(3):1117-26
5*	J:199568 Neufeld SJ, Zhou X, Vize PD, Cobb J, mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos. Dev Dyn. 2013 Sep;242(9):1094-100
2*	J:61158 Ngo-Muller V, Muneoka K, Influence of FGF4 on digit morphogenesis during limb development in the mouse. Dev Biol. 2000 Mar 15;219(2):224-36
2	J:237505 Norrie JL, Li Q, Co S, Huang BL, Ding D, Uy JC, Ji Z, Mackem S, Bedford MT, Galli A, Ji H, Vokes SA, PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud. Development. 2016 Dec 15;143(24):4608-4619
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
3	J:78407 O'Rourke MP, Soo K, Behringer RR, Hui CC, Tam PP, Twist plays an essential role in FGF and SHH signal transduction during mouse limb development. Dev Biol. 2002 Aug 1;248(1):143-56
4	J:30669 Oefelein M, Chin-Chance C, Bushman W, Expression of the homeotic gene Hox-d13 in the developing and adult mouse prostate. J Urol. 1996 Jan;155(1):342-6
4	J:74219 Ogino Y, Suzuki K, Haraguchi R, Satoh Y, Dolle P, Yamada G, External genitalia formation: role of fibroblast growth factor, retinoic acid signaling, and distal urethral epithelium. Ann N Y Acad Sci. 2001 Dec;948:13-31
1	J:144308 Ovchinnikov DA, Selever J, Wang Y, Chen YT, Mishina Y, Martin JF, Behringer RR, BMP receptor type IA in limb bud mesenchyme regulates distal outgrowth and patterning. Dev Biol. 2006 Jul 1;295(1):103-15
1	J:101476 Panman L, Drenth T, Tewelscher P, Zuniga A, Zeller R, Genetic interaction of Gli3 and Alx4 during limb development. Int J Dev Biol. 2005;49(4):443-8
1	J:112237 Panman L, Galli A, Lagarde N, Michos O, Soete G, Zuniga A, Zeller R, Differential regulation of gene expression in the digit forming area of the mouse limb bud by SHH and gremlin 1/FGF-mediated epithelial-mesenchymal signalling. Development. 2006 Sep;133(17):3419-28
2	J:49154 Partanen J, Schwartz L, Rossant J, Opposite phenotypes of hypomorphic and Y766 phosphorylation site mutations reveal a function for Fgfr1 in anteroposterior patterning of mouse embryos. Genes Dev. 1998 Aug 1;12(15):2332-44
4*	J:89197 Patterson LT, Potter SS, Atlas of Hox gene expression in the developing kidney. Dev Dyn. 2004 Apr;229(4):771-9
1	J:147584 Patterson VL, Damrau C, Paudyal A, Reeve B, Grimes DT, Stewart ME, Williams DJ, Siggers P, Greenfield A, Murdoch JN, Mouse hitchhiker mutants have spina bifida, dorso-ventral patterning defects and polydactyly: identification of Tulp3 as a novel negative regulator of the Sonic hedgehog pathway. Hum Mol Genet. 2009 May 15;18(10):1719-39
1*	J:43311 Peichel CL, Prabhakaran B, Vogt TF, The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning. Development. 1997 Sep;124(18):3481-92
2*	J:157955 Pennimpede T, Cameron DA, MacLean GA, Petkovich M, Analysis of Cyp26b1/Rarg compound-null mice reveals two genetically separable effects of retinoic acid on limb outgrowth. Dev Biol. 2010 Mar 1;339(1):179-86
6*	J:77812 Perriton CL, Powles N, Chiang C, Maconochie MK, Cohn MJ, Sonic hedgehog signaling from the urethral epithelium controls external genital development. Dev Biol. 2002 Jul 1;247(1):26-46
3*	J:54823 Podlasek CA, Clemens JQ, Bushman W, Hoxa-13 gene mutation results in abnormal seminal vesicle and prostate development. J Urol. 1999 May;161(5):1655-61
2*	J:56986 Post LC, Innis JW, Altered Hox expression and increased cell death distinguish Hypodactyly from Hoxa13 null mice. Int J Dev Biol. 1999 Jul;43(4):287-94
1	J:338811 Qu F, Li W, Xu J, Zhang R, Ke J, Ren X, Meng X, Qin L, Zhang J, Lu F, Zhou X, Luo X, Zhang Z, Wang M, Wu G, Pei D, Chen J, Cui G, Suo S, Peng G, Three-dimensional molecular architecture of mouse organogenesis. Nat Commun. 2023 Jul 31;14(1):4599
1	J:43769 Qu S, Niswender KD, Ji Q, van der Meer R, Keeney D, Magnuson MA , Wisdom R, Polydactyly and ectopic ZPA formation in Alx-4 mutant mice. Development. 1997 Oct;124(20):3999-4008
1	J:239799 Raines AM, Magella B, Adam M, Potter SS, Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development. BMC Dev Biol. 2015 Jul 19;15:28
1	J:134490 Raz R, Stricker S, Gazzerro E, Clor JL, Witte F, Nistala H, Zabski S, Pereira RC, Stadmeyer L, Wang X, Gowen L, Sleeman MW, Yancopoulos GD, Canalis E, Mundlos S, Valenzuela DM, Economides AN, The mutation ROR2W749X, linked to human BDB, is a recessive mutation in the mouse, causing brachydactyly, mediating patterning of joints and modeling recessive Robinow syndrome. Development. 2008 May;135(9):1713-23
2	J:118803 Ribes V, Otto DM, Dickmann L, Schmidt K, Schuhbaur B, Henderson C, Blomhoff R, Wolf CR, Tickle C, Dolle P, Rescue of cytochrome P450 oxidoreductase (Por) mouse mutants reveals functions in vasculogenesis, brain and limb patterning linked to retinoic acid homeostasis. Dev Biol. 2007 Mar 1;303(1):66-81
1*	J:336421 Rodriguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D, Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol. 2019 Jul 12;17(1):55
2	J:260451 Rodriguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D, The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281
1	J:180121 Ruf S, Symmons O, Uslu VV, Dolle D, Hot C, Ettwiller L, Spitz F, Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet. 2011 Apr;43(4):379-86
1	J:290220 Sato T, Kataoka K, Ito Y, Yokoyama S, Inui M, Mori M, Takahashi S, Akita K, Takada S, Ueno-Kudoh H, Asahara H, Lin28a/let-7 pathway modulates the Hox code via Polycomb regulation during axial patterning in vertebrates. Elife. 2020 May 29;9:e53608
1	J:239094 Schep R, Necsulea A, Rodriguez-Carballo E, Guerreiro I, Andrey G, Nguyen Huynh TH, Marcet V, Zakany J, Duboule D, Beccari L, Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7720-E7729
2*	J:172713 Schorderet P, Duboule D, Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011 May;7(5):e1002071
1	J:158139 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development. 2009 Aug;136(15):2643-51
1	J:128571 Selever J, Liu W, Lu MF, Behringer RR, Martin JF, Bmp4 in limb bud mesoderm regulates digit pattern by controlling AER development. Dev Biol. 2004 Dec 15;276(2):268-79
1	J:52453 Sharpe J, Lettice L, Hecksher-Sorensen J, Fox M, Hill R, Krumlauf R, Identification of sonic hedgehog as a candidate gene responsible for the polydactylous mouse mutant Sasquatch. Curr Biol. 1999 Jan 28;9(2):97-100
2	J:241710 Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson HL, Stadler HS, Visel A, Drouin J, Kmita M, Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep. 2016 Dec 13;17(11):2913-2926
3*	J:204375 Sheth R, Bastida MF, Kmita M, Ros M, "Self-regulation," a new facet of Hox genes' function. Dev Dyn. 2014 Jan;243(1):182-91
1	J:192010 Sheth R, Marcon L, Bastida MF, Junco M, Quintana L, Dahn R, Kmita M, Sharpe J, Ros MA, Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism. Science. 2012 Dec 14;338(6113):1476-80
1	J:57316 Sidow A, Bulotsky MS, Kerrebrock AW, Birren BW, Altshuler D, Jaenisch R, Johnson KR, Lander ES, A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant. Nat Genet. 1999 Sep;23(1):104-7
1	J:137353 Sohaskey ML, Yu J, Diaz MA, Plaas AH, Harland RM, JAWS coordinates chondrogenesis and synovial joint positioning. Development. 2008 Jul;135(13):2215-20
1	J:169050 Soshnikova N, Montavon T, Leleu M, Galjart N, Duboule D, Functional analysis of CTCF during mammalian limb development. Dev Cell. 2010 Dec 14;19(6):819-30
3	J:83372 Spitz F, Gonzalez F, Duboule D, A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 2003 May 2;113(3):405-17
1	J:71405 Spitz F, Gonzalez F, Peichel C, Vogt TF, Duboule D, Zakany J, Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev. 2001 Sep 1;15(17):2209-14
1	J:205284 Storer M, Mas A, Robert-Moreno A, Pecoraro M, Ortells MC, Di Giacomo V, Yosef R, Pilpel N, Krizhanovsky V, Sharpe J, Keyes WM, Senescence is a developmental mechanism that contributes to embryonic growth and patterning. Cell. 2013 Nov 21;155(5):1119-30
1	J:78402 Sun X, Mariani FV, Martin GR, Functions of FGF signalling from the apical ectodermal ridge in limb development. Nature. 2002 Aug 1;418(6897):501-8
2	J:154460 Suzuki D, Yamada A, Amano T, Yasuhara R, Kimura A, Sakahara M, Tsumaki N, Takeda S, Tamura M, Nakamura M, Wada N, Nohno T, Shiroishi T, Aiba A, Kamijo R, Essential mesenchymal role of small GTPase Rac1 in interdigital programmed cell death during limb development. Dev Biol. 2009 Nov 15;335(2):396-406
1	J:207496 Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F, Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014 Mar;24(3):390-400
1	J:53310 Szeto DP, Rodriguez-Esteban C, Ryan AK, O'Connell SM, Liu F, Kioussi C, Gleiberman AS, Izpisua-Belmonte JC, Rosenfeld MG, Role of the Bicoid-related homeodomain factor Pitx1 in specifying hindlimb morphogenesis and pituitary development. Genes Dev. 1999 Feb 15;13(4):484-94
2*	J:45575 Takagi T, Moribe H, Kondoh H, Higashi Y, DeltaEF1, a zinc finger and homeodomain transcription factor, is required for skeleton patterning in multiple lineages. Development. 1998 Jan;125(1):21-31
3	J:105255 Tarchini B, Duboule D, Control of Hoxd genes' collinearity during early limb development. Dev Cell. 2006 Jan;10(1):93-103
1	J:79710 te Welscher P, Zuniga A, Kuijper S, Drenth T, Goedemans HJ, Meijlink F, Zeller R, Progression of vertebrate limb development through SHH-mediated counteraction of GLI3. Science. 2002 Oct 25;298(5594):827-30
2*	J:50488 ten Berge D, Brouwer A, Korving J, Martin JF, Meijlink F, Prx1 and Prx2 in skeletogenesis: roles in the craniofacial region, inner ear and limbs. Development. 1998 Oct;125(19):3831-42
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
2*	J:306252 Tissieres V, Geier F, Kessler B, Wolf E, Zeller R, Lopez-Rios J, Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits. Cell Rep. 2020 Apr 7;31(1):107490
1	J:111607 Tribioli C, Lufkin T, Bapx1 homeobox gene gain-of-function mice show preaxial polydactyly and activated Shh signaling in the developing limb. Dev Dyn. 2006 Jun 21;235(9):2483-2492
4	J:317370 Trofka A, Huang BL, Zhu J, Heinz WF, Magidson V, Shibata Y, Shi YB, Tarchini B, Stadler HS, Kabangu M, Al Haj Baddar NW, Voss SR, Mackem S, Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Curr Biol. 2021 Nov 22;31(22):4923-4934.e5
3	J:170557 Tschopp P, Duboule D, A regulatory 'landscape effect' over the HoxD cluster. Dev Biol. 2011 Mar 15;351(2):288-96
4	J:146752 Tschopp P, Tarchini B, Spitz F, Zakany J, Duboule D, Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genet. 2009 Mar;5(3):e1000398
2	J:180902 van de Ven C, Bialecka M, Neijts R, Young T, Rowland JE, Stringer EJ, Van Rooijen C, Meijlink F, Novoa A, Freund JN, Mallo M, Beck F, Deschamps J, Concerted involvement of Cdx/Hox genes and Wnt signaling in morphogenesis of the caudal neural tube and cloacal derivatives from the posterior growth zone. Development. 2011 Aug;138(16):3451-62
1*	J:33879 van der Hoeven F, Zakany J, Duboule D, Gene transpositions in the HoxD complex reveal a hierarchy of regulatory controls. Cell. 1996 Jun 28;85(7):1025-35
3	J:101736 Verheyden JM, Lewandoski M, Deng C, Harfe BD, Sun X, Conditional inactivation of Fgfr1 in mouse defines its role in limb bud establishment, outgrowth and digit patterning. Development. 2005 Oct;132(19):4235-45
3	J:161451 Villavicencio-Lorini P, Kuss P, Friedrich J, Haupt J, Farooq M, Turkmen S, Duboule D, Hecht J, Mundlos S, Homeobox genes d11-d13 and a13 control mouse autopod cortical bone and joint formation. J Clin Invest. 2010 Jun 1;120(6):1994-2004
1*	J:118340 Wang C, Pan Y, Wang B, A hypermorphic mouse Gli3 allele results in a polydactylous limb phenotype. Dev Dyn. 2007 Mar;236(3):769-76
1*	J:121609 Wang C, Ruther U, Wang B, The Shh-independent activator function of the full-length Gli3 protein and its role in vertebrate limb digit patterning. Dev Biol. 2007 May 15;305(2):460-9
1*	J:171189 Wang CK, Tsugane MH, Scranton V, Kosher RA, Pierro LJ, Upholt WB, Dealy CN, Pleiotropic patterning response to activation of Shh signaling in the limb apical ectodermal ridge. Dev Dyn. 2011 May;240(5):1289-302
2	J:330212 Wang S, Tanaka Y, Xu Y, Takeda S, Hirokawa N, KIF3B promotes a PI3K signaling gradient causing changes in a Shh protein gradient and suppressing polydactyly in mice. Dev Cell. 2022 Oct 10;57(19):2273-2289.e11
1*	J:326556 Wang Y, Yasmin L, Li L, Gao P, Xu X, Sun X, Godbout R, DDX1 vesicles control calcium-dependent mitochondrial activity in mouse embryos. Nat Commun. 2022 Jul 1;13(1):3794
3	J:44837 Warot X, Fromental-Ramain C, Fraulob V, Chambon P, Dolle P, Gene dosage-dependent effects of the Hoxa-13 and Hoxd-13 mutations on morphogenesis of the terminal parts of the digestive and urogenital tracts. Development. 1997 Dec;124(23):4781-91
3	J:112886 Williams ME, Lehoczky JA, Innis JW, A group 13 homeodomain is neither necessary nor sufficient for posterior prevalence in the mouse limb. Dev Biol. 2006 Sep 15;297(2):493-507
4	J:95882 Williams TM, Williams ME, Innis JW, Range of HOX/TALE superclass associations and protein domain requirements for HOXA13:MEIS interaction. Dev Biol. 2005 Jan 15;277(2):457-71
1*	J:96550 Williams TM, Williams ME, Kuick R, Misek D, McDonagh K, Hanash S, Innis JW, Candidate downstream regulated genes of HOX group 13 transcription factors with and without monomeric DNA binding capability. Dev Biol. 2005 Mar 15;279(2):462-80
1*	J:316988 Williamson I, Eskeland R, Lettice LA, Hill AE, Boyle S, Grimes GR, Hill RE, Bickmore WA, Anterior-posterior differences in HoxD chromatin topology in limb development. Development. 2012 Sep;139(17):3157-67
1	J:226712 Wong SF, Agarwal V, Mansfield JH, Denans N, Schwartz MG, Prosser HM, Pourquie O, Bartel DP, Tabin CJ, McGlinn E, Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4884-93
1	J:242833 Wu C, Li J, Peterson A, Tao K, Wang B, Loss of dynein-2 intermediate chain Wdr34 results in defects in retrograde ciliary protein trafficking and Hedgehog signaling in the mouse. Hum Mol Genet. 2017 Jul 01;26(13):2386-2397
3	J:175770 Wyngaarden LA, Delgado-Olguin P, Su IH, Bruneau BG, Hopyan S, Ezh2 regulates anteroposterior axis specification and proximodistal axis elongation in the developing limb. Development. 2011 Sep;138(17):3759-67
1	J:203059 Xu B, Hrycaj SM, McIntyre DC, Baker NC, Takeuchi JK, Jeannotte L, Gaber ZB, Novitch BG, Wellik DM, Hox5 interacts with Plzf to restrict Shh expression in the developing forelimb. Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19438-43
2	J:170090 Xu B, Wellik DM, Axial Hox9 activity establishes the posterior field in the developing forelimb. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4888-91
2	J:56002 Xu X, Weinstein M, Li C, Deng C, Fibroblast growth factor receptors (FGFRs) and their roles in limb development. Cell Tissue Res. 1999 Apr;296(1):33-43
1	J:268053 Yakushiji-Kaminatsui N, Lopez-Delisle L, Bolt CC, Andrey G, Beccari L, Duboule D, Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. PLoS Biol. 2018 Nov;16(11):e3000004
2*	J:52600 Yamaguchi TP, Bradley A, McMahon AP, Jones S, A Wnt5a pathway underlies outgrowth of multiple structures in the vertebrate embryo. Development. 1999 Mar;126(6):1211-23
1*	J:49653 Yang Y, Guillot P, Boyd Y, Lyon MF, McMahon AP, Evidence that preaxial polydactyly in the Doublefoot mutant is due to ectopic Indian Hedgehog signaling. Development. 1998 Aug;125(16):3123-32
4	J:89029 Yashiro K, Zhao X, Uehara M, Yamashita K, Nishijima M, Nishino J, Saijoh Y, Sakai Y, Hamada H, Regulation of retinoic acid distribution is required for proximodistal patterning and outgrowth of the developing mouse limb. Dev Cell. 2004 Mar;6(3):411-22
1	J:312414 Yogosawa S, Ohkido M, Horii T, Okazaki Y, Nakayama J, Yoshida S, Toyokuni S, Hatada I, Morimoto M, Yoshida K, Mice lacking DYRK2 exhibit congenital malformations with lung hypoplasia and altered Foxf1 expression gradient. Commun Biol. 2021 Oct 20;4(1):1204
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
4	J:154781 Young T, Rowland JE, van de Ven C, Bialecka M, Novoa A, Carapuco M, van Nes J, de Graaff W, Duluc I, Freund JN, Beck F, Mallo M, Deschamps J, Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos. Dev Cell. 2009 Oct;17(4):516-26
2	J:127046 Zacchetti G, Duboule D, Zakany J, Hox gene function in vertebrate gut morphogenesis: the case of the caecum. Development. 2007 Nov;134(22):3967-3973
5	J:91567 Zakany J, Kmita M, Duboule D, A dual role for Hox genes in limb anterior-posterior asymmetry. Science. 2004 Jun 11;304(5677):1669-72
1	J:122561 Zakany J, Zacchetti G, Duboule D, Interactions between HOXD and Gli3 genes control the limb apical ectodermal ridge via Fgf10. Dev Biol. 2007 Jun 15;306(2):883-93
2	J:159120 Zeng H, Hoover AN, Liu A, PCP effector gene Inturned is an important regulator of cilia formation and embryonic development in mammals. Dev Biol. 2010 Mar 15;339(2):418-28
4	J:83305 Zhang Q, Murcia NS, Chittenden LR, Richards WG, Michaud EJ, Woychik RP, Yoder BK, Loss of the Tg737 protein results in skeletal patterning defects. Dev Dyn. 2003 May;227(1):78-90
1	J:225113 Zhang Y, Liu Z, Medrzycki M, Cao K, Fan Y, Reduction of Hox gene expression by histone H1 depletion. PLoS One. 2012;7(6):e38829
2	J:149477 Zhang Z, Verheyden JM, Hassell JA, Sun X, FGF-regulated Etv genes are essential for repressing Shh expression in mouse limb buds. Dev Cell. 2009 Apr;16(4):607-13
3	J:61723 Zhang Z, Yu X, Zhang Y, Geronimo B, Lovlie A, Fromm SH, Chen Y, Targeted misexpression of constitutively active BMP receptor-IB causes bifurcation, duplication, and posterior transformation of digit in mouse limb. Dev Biol. 2000 Apr 15;220(2):154-67
1	J:200718 Zhou W, Zhu H, Zhao J, Li H, Wan Y, Cao J, Zhao H, Yu J, Zhou R, Yao Y, Zhang L, Wang L, He L, Ma G, Yao Z, Guo X, Misexpression of Pknox2 in mouse limb bud mesenchyme perturbs zeugopod development and deltoid crest formation. PLoS One. 2013;8(5):e64237
1*	J:187603 Zhu H, Zhao J, Zhou W, Li H, Zhou R, Zhang L, Zhao H, Cao J, Zhu X, Hu H, Ma G, He L, Yao Z, Yao L, Guo X, Ndrg2 regulates vertebral specification in differentiating somites. Dev Biol. 2012 Sep 15;369(2):308-18
1	J:184918 Zhu X, Zhu H, Zhang L, Huang S, Cao J, Ma G, Feng G, He L, Yang Y, Guo X, Wls-mediated Wnts differentially regulate distal limb patterning and tissue morphogenesis. Dev Biol. 2012 May 15;365(2):328-38
1	J:257510 Zhu XJ, Fang Y, Xiong Y, Wang M, Yang X, Li Y, Zhang X, Dai ZM, Qiu M, Zhang Z, Zhang Z, Disruption of Wnt production in Shh lineage causes bone malformation in mice, mimicking human Malik-Percin-type syndactyly. FEBS Lett. 2018 Feb;592(3):356-368
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
1*	J:76826 Zuniga A, Quillet R, Perrin-Schmitt F, Zeller R, Mouse Twist is required for fibroblast growth factor-mediated epithelial-mesenchymal signalling and cell survival during limb morphogenesis. Mech Dev. 2002 Jun;114(1-2):51
2*	J:49322 Zuniga A, Zeller R, Gli3 (Xt) and formin (ld) participate in the positioning of the polarising region and control of posterior limb-bud identity. Development. 1999 Jan;126(1):13-21