82
C. Rochette-Egly
Cholley PE, Moehlin J, Rohmer A, Zilliox V, Nicaise S, Gronemeyer H, Mendoza-Parra MA (2018)
Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators.
NPJ Syst Biol Appl 4:29
Cunningham TJ, Duester G (2015) Mechanisms of retinoic acid signalling and its roles in organ
and limb development. Nat Rev Mol Cell Biol 16:110–123
Davidson EH (2002) A genomic regulatory network for development. Sci 295(5560):1669–1678
Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, Bertin I, Jost B, Davidson
I (2010) Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic
fibroblasts and embryonic stem cells. Mol Cell Biol 30:231–244
Dirks RA, Stunnenberg HG, Marks H (2016) Genome-wide epigenomic profiling for biomarker
discovery. Clin Epigenetics 8:122
Dolle P, Ruberte E, Kastner P, Petkovich M, Stoner CM, Gudas LJ, Chambon P (1989) Differential
expression of genes encoding alpha, beta and gamma retinoic acid receptors and CRABP in the
developing limbs of the mouse. Nature 342:702–705
Dolle P, Ruberte E, Leroy P, Morriss-Kay G, Chambon P (1990) Retinoic acid receptors and cellular
retinoid binding proteins. I. A systematic study of their differential pattern of transcription during
mouse organogenesis. Development 110:1133–1151
Eifert C, Sangster-Guity N, Yu LM, Chittur SV, Perez AV, Tine JA, McCormick PJ (2006) Global
gene expression profiles associated with retinoic acid-induced differentiation of embryonal
carcinoma cells. Mol Reprod Dev 73:796–824
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z (2007) Reconstructing dynamic regulatory
maps. Mol Syst Biol 3:74
Fathi A, Hatami M, Hajihosseini V, Fattahi F, Kiani S, Baharvand H, Salekdeh GH (2011) Comprehensive gene expression analysis of human embryonic stem cells during differentiation into
neural cells. PLoS ONE 6:e22856
Freemantle SJ, Kerley JS, Olsen SL, Gross RH, Spinella MJ (2002) Developmentally-related candidate retinoic acid target genes regulated early during neuronal differentiation of human embryonal
carcinoma. Oncogene 21:2880–2889
Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize
protein-DNA interactions. Nat Rev Genet 13:840–852
Gardini A (2017) Global Run-On Sequencing (GRO-Seq). Methods Mol Biol 1468:111–120
Giguere V, Lyn S, Yip P, Siu CH, Amin S (1990) Molecular cloning of cDNA encoding a second
cellular retinoic acid-binding protein. Proc Natl Acad Sci U S A 87:6233–6237
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome
Res 17:877–885
Harris TM, Childs G (2002) Global gene expression patterns during differentiation of F9 embryonal
carcinoma cells into parietal endoderm. Funct Integr Genomics 2:105–119
Hermsen SA, Pronk TE, van den Brandhof EJ, van der Ven LT, Piersma AH (2013) Transcriptomic
analysis in the developing zebrafish embryo after compound exposure: individual gene expression
and pathway regulation. Toxicol Appl Pharmacol 272:161–171
Hogan BL, Taylor A, Adamson E (1981) Cell interactions modulate embryonal carcinoma cell
differentiation into parietal or visceral endoderm. Nature 291:235–237
Hu L, Gudas LJ (1990) Cyclic AMP analogs and retinoic acid influence the expression of retinoic
acid receptor alpha, beta, and gamma mRNAs in F9 teratocarcinoma cells. Mol Cell Biol 10:391–
396
Jarvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O (2004) Are
data from different gene expression microarray platforms comparable? Genomics 83:1164–1168
Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK (2001) Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci
U S A 98:218–223
C. Rochette-Egly
Cholley PE, Moehlin J, Rohmer A, Zilliox V, Nicaise S, Gronemeyer H, Mendoza-Parra MA (2018)
Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators.
NPJ Syst Biol Appl 4:29
Cunningham TJ, Duester G (2015) Mechanisms of retinoic acid signalling and its roles in organ
and limb development. Nat Rev Mol Cell Biol 16:110–123
Davidson EH (2002) A genomic regulatory network for development. Sci 295(5560):1669–1678
Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, Bertin I, Jost B, Davidson
I (2010) Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic
fibroblasts and embryonic stem cells. Mol Cell Biol 30:231–244
Dirks RA, Stunnenberg HG, Marks H (2016) Genome-wide epigenomic profiling for biomarker
discovery. Clin Epigenetics 8:122
Dolle P, Ruberte E, Kastner P, Petkovich M, Stoner CM, Gudas LJ, Chambon P (1989) Differential
expression of genes encoding alpha, beta and gamma retinoic acid receptors and CRABP in the
developing limbs of the mouse. Nature 342:702–705
Dolle P, Ruberte E, Leroy P, Morriss-Kay G, Chambon P (1990) Retinoic acid receptors and cellular
retinoid binding proteins. I. A systematic study of their differential pattern of transcription during
mouse organogenesis. Development 110:1133–1151
Eifert C, Sangster-Guity N, Yu LM, Chittur SV, Perez AV, Tine JA, McCormick PJ (2006) Global
gene expression profiles associated with retinoic acid-induced differentiation of embryonal
carcinoma cells. Mol Reprod Dev 73:796–824
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z (2007) Reconstructing dynamic regulatory
maps. Mol Syst Biol 3:74
Fathi A, Hatami M, Hajihosseini V, Fattahi F, Kiani S, Baharvand H, Salekdeh GH (2011) Comprehensive gene expression analysis of human embryonic stem cells during differentiation into
neural cells. PLoS ONE 6:e22856
Freemantle SJ, Kerley JS, Olsen SL, Gross RH, Spinella MJ (2002) Developmentally-related candidate retinoic acid target genes regulated early during neuronal differentiation of human embryonal
carcinoma. Oncogene 21:2880–2889
Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize
protein-DNA interactions. Nat Rev Genet 13:840–852
Gardini A (2017) Global Run-On Sequencing (GRO-Seq). Methods Mol Biol 1468:111–120
Giguere V, Lyn S, Yip P, Siu CH, Amin S (1990) Molecular cloning of cDNA encoding a second
cellular retinoic acid-binding protein. Proc Natl Acad Sci U S A 87:6233–6237
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome
Res 17:877–885
Harris TM, Childs G (2002) Global gene expression patterns during differentiation of F9 embryonal
carcinoma cells into parietal endoderm. Funct Integr Genomics 2:105–119
Hermsen SA, Pronk TE, van den Brandhof EJ, van der Ven LT, Piersma AH (2013) Transcriptomic
analysis in the developing zebrafish embryo after compound exposure: individual gene expression
and pathway regulation. Toxicol Appl Pharmacol 272:161–171
Hogan BL, Taylor A, Adamson E (1981) Cell interactions modulate embryonal carcinoma cell
differentiation into parietal or visceral endoderm. Nature 291:235–237
Hu L, Gudas LJ (1990) Cyclic AMP analogs and retinoic acid influence the expression of retinoic
acid receptor alpha, beta, and gamma mRNAs in F9 teratocarcinoma cells. Mol Cell Biol 10:391–
396
Jarvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O (2004) Are
data from different gene expression microarray platforms comparable? Genomics 83:1164–1168
Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK (2001) Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci
U S A 98:218–223