Olivera DJ, Nikolaub B, Wurtelea ES. Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metab Eng. 2002;4(1):98–106.
Article
Google Scholar
Scott MP. Development: the natural history of genes. Cell. 2000;100(1):27–40.
Article
CAS
PubMed
Google Scholar
Amrani N, Sachs MS, Jacobson A. Early nonsense: mRNA decay solves a translational problem. Nat Rev Mol Cell Biol. 2006;7:415–25.
Article
CAS
PubMed
Google Scholar
Sanguinetti G, Lawrence ND, Rattray M. Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities. Bioinformatics. 2006;22(22):2755–81.
Article
Google Scholar
Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinf. 2007;8:452.
Article
Google Scholar
Strick TR, Croquette V, Bensimon D. Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature. 2000;404:901–4.
Article
CAS
PubMed
Google Scholar
Jagannathan I, Cole HA, Hayes JJ. Base excision repair in nucleosome substrates. Chromosome Res. 2006;14:27–37.
Article
CAS
PubMed
Google Scholar
Sonehara H, Nagata M, Aoki F. Roles of the first and second round of DNA replication in the regulation of zygotic gene activation in mice. J Reprod Dev. 2008;54(5):381–4.
Article
CAS
PubMed
Google Scholar
Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet. 2007;8:533–43.
Article
CAS
PubMed
Google Scholar
Anderson P, Kedersha N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat Rev Mol Cell Biol. 2009;10:430–6.
Article
CAS
PubMed
Google Scholar
Brogna S, Wen J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol. 2009;16:107–13.
Article
CAS
PubMed
Google Scholar
Marko-Varga G. Pathway proteomics: global and focused approaches. Am J Pharmacogenomics. 2005;5(2):113–22.
Article
CAS
PubMed
Google Scholar
Gardner TS, Faith JJ. Reverse-engineering transcription control networks. Phys Life Rev. 2005;2(1):65–88.
Article
PubMed
Google Scholar
Bansal M, Belcastro V, Ambesi-Impiombato A, Bernardo D. How to infer gene networks from expression profiles. Mol Syst Biol. 2007;3(78):78–87.
PubMed
PubMed Central
Google Scholar
Herrgård MJ, Lee B-S, Portnoy V, Palsson BØ. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res. 2006;16(5):627–35.
Article
PubMed
PubMed Central
Google Scholar
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, et al. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol. 2008;4(3):e1000021.
Article
PubMed
PubMed Central
Google Scholar
Ye C, Galbraith SJ, Liao JC, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol. 2009;5(3):e1000311.
Article
PubMed
PubMed Central
Google Scholar
Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in saccharomyces cerevisiae. Mol Syst Biol. 2007;3:153.
Article
PubMed
PubMed Central
Google Scholar
Gatta GD, Bansal M, Ambesi-Impiombato A, Antonini D, Missero C, Bernardo D. Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome Res. 2008;18(6):939–48.
Article
PubMed
PubMed Central
Google Scholar
Cai B, Chang SH, Becker EBE, Bonni A, Xia Z. p38 MAP kinase mediates apoptosis through phosphorylation of BimEL at ser-65. J Biol Chem. 2006;281(35):25215–22.
Article
CAS
PubMed
Google Scholar
Oliveira AP, Patil KR, Nielsen J. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst Biol. 2008;2:17.
Article
PubMed
PubMed Central
Google Scholar
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, KLindblad-Toh V, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3’ UTRs by comparison of several mammals. Nature. 2005;434:338–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanguinetti G, Lawrence ND, Rattray M. A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription. Bioinformatics. 2006;22(14):1753–9.
Article
CAS
PubMed
Google Scholar
Driever W, Thoma G, Nüsslein-Volhard C. Determination of spatial domains of zygotic gene expression in the drosophila embryo by the affinity of binding sites for the bicoid morphogen. Nature. 1989;340:363–7.
Article
CAS
PubMed
Google Scholar
Liao JC, Boscolo R, Yang Y-L, Tran LM, Sabatti C, Roychowdhury VP. Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci. 2003;100(26):15522–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alter O, Golub GH. Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci. 2004;101:16577–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao F, Foat BC, Bussemaker HJ. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinforma. 2004;5(31):31.
Article
Google Scholar
Boulesteix A-L, Strimmer K. Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model. 2005;2(23):23.
Article
PubMed
PubMed Central
Google Scholar
Kim HD, Shay T, O’Shea EK, Regev A. Transcriptional regulatory circuits - predicting numbers from alphabets. Science. 2009;325:429–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Honkela A, Girardot C, Gustafson EH, Liu Y-H, Furlong EEM, Lawrence ND, Rattray M. Model-based method for transcription factor target identification with limited data. Proc Natl Acad Sci U S A. 2010;107(17):7793–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012;489(7414):91–100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buck MJ, Lie JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 2004;83(3):349–60.
Article
CAS
PubMed
Google Scholar
Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10(10):669–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu Z, Shendure J, Church GM. Discovering functional transcription-factor combinations in the human cell cycle. Genome Res. 2005;15:848–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang L-W, Nagarajan R, Magee JA, Milbrandt J, Stormo GD. A systematic model to predict transcriptional regulatory. Genome Res. 2006;16:405–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davies SR, Chang L-W, Patra D, Xing X, Posey K, Hecht J, Stormo GD, Sandell LJ. Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. Genome Res. 2007;17:1438–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hui L, Bakiri L, Mairhorfer A, Schweifer N, Haslinger C, Kenner L, Komnenovic V, Scheuch H, Beug H, Wagne EF. p38alpha suppresses normal and cancer cell proliferation by antagonizing the JNK–c-Jun pathway. Nat Genet. 2007;39:741–9.
Article
CAS
PubMed
Google Scholar
Lin JX, Li P, Liu D, Jin HT, He J, Ata Ur Rasheed M, Rochman Y, Wang L, Cui K, Liu C, et al. Critical role of STAT5 transcription factor tetramerization for cytokine responses and normal immune function. Immunity. 2012;36:586–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
Smet RD, Marchal K. Advantages and limitations of current network inference methods. Nat Rev Microbiol. 2010;8(10):717–29.
PubMed
Google Scholar
Perkins ND. Integrating cell-signalling pathways with NF-kappaB and IKK function. Nat Rev Mol Cell Bio. 2007;8:49–62.
Article
CAS
Google Scholar
Brichese L, Cazettes G, Valette A. JNK is associated with Bcl-2 and PP1 in mitochondria: paclitaxel induces its activation and its association with the phosphorylated form of Bcl-2. Cell Cycle. 2004;3(10):1312–9.
Article
CAS
PubMed
Google Scholar
Wagner EF, Nebreda ÁR. Signal integration by JNK and p38 MAPK pathways in cancer development. Nat Rev Cancer. 2009;9(8):537–49.
Article
CAS
PubMed
Google Scholar
Brivanlou AH, Jr JED. Signal transduction and the control of gene expression. Science. 2002;295(5556):813–8.
Article
CAS
PubMed
Google Scholar
Behren A, Muhlen S, Sanhueza GAA, Schwager C, Plinkert PK, Huber PE, Abdollahi A, Simon C. Phenotype-assisted transcriptome analysis identifies FOXM1 downstream from Ras-MKK3-p38 to regulate in vitro cellular invasion. Oncogene. 2010;29(10):1519–30.
Article
CAS
PubMed
Google Scholar
Sanchez-Calderon H, Rosa LR-d, Milo M, Pichel JG, Holley M, Varela-Nieto I. RNA microarray analysis in prenatal mouse cochlea reveals novel IGF-I target genes: implication of MEF2 and FOXM1 transcription factors. PLoS One. 2010;5(1):e8699.
Article
PubMed
PubMed Central
Google Scholar
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science. 2010;328(5981):1036–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
McMaster A, Jangani M, Sommer P, Han N, Brass A, Beesley S, Lu W, Berry A, Loudon A, Donn R, et al. Ultradian cortisol pulsatility encodes a distinct, biologically important signal. PLoS One. 2011;6(1):e15766.
Article
CAS
PubMed
PubMed Central
Google Scholar
Han N, Dol Z, Vasieva O, Hyde R, Liloglou T, Raji O, Brambilla E, Brambilla C, Martinet Y, Sozzi G, et al. Progressive lung cancer determined by expression profiling and transcriptional regulation. Int J Oncol. 2012;41(1):242–52.
CAS
PubMed
Google Scholar
Darieva Z, Han N, Warwood S, Doris KS, Morgan BA, Sharrocks AD. Protein kinase C regulates late cell cycle-dependent gene expression. Mol Cell Biol. 2012;32(22):4651–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Papa S, Bubici C, Zazzeroni F, Pham CG, Kuntzen C, Knabb JR, Dean K, Franzoso G. The NF-kappaB-mediated control of the JNK cascade in the antagonism of programmed cell death in health and disease. Cell Death Differ. 2006;13:712–29.
Article
CAS
PubMed
Google Scholar
Guo F, Tanzer S, Busslinger M, Weih F. Lack of nuclear factor-kappa B2/p100 causes a RelB-dependent block in early B lymphopoiesis. Blood. 2008;112(3):551–9.
Article
CAS
PubMed
Google Scholar
Thonel A, Vandekerckhove J, Lanneau D, Selvakumar S, Courtois G, Hazoume A, Brunet M, Maurel S, Hammann A, Ribeil JA, et al. HSP27 controls GATA-1 protein level during erythroid cell differentiation. Blood. 2010;116(1):85–96.
Article
PubMed
Google Scholar
Stassen M, Klein M, Becker M, Bopp T, Neudorfl C, Richter C, Heib V, Klein-Hessling S, Serfling E, Schild H, et al. p38 MAP kinase drives the expression of mast cell-derived IL-9 via activation of the transcription factor GATA-1. Mol Immunol. 2007;44(5):926–33.
Article
CAS
PubMed
Google Scholar
Angelis L, Zhao J, Andreucci JJ, Olson EN, McDermott GCJC. Regulation of vertebrate myotome development by the p38 MAP kinase–MEF2 signaling pathway. Dev Biol. 2005;283(1):171–9.
Article
PubMed
Google Scholar
Ramsauer K, Sadzak I, Porras A, Pilz A, Nebreda AR, Decker T, Kovarik P. p38 MAPK enhances STAT1-dependent transcription independently of Ser-727 phosphorylation. Proc Natl Acad Sci. 2002;99(20):12859–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bradham C, McClay DR. p38 MAPK in development and cancer. Cell Cycle. 2006;5(8):824–8.
Article
CAS
PubMed
Google Scholar
Li S, Gallup M, Chen Y-T, McNamara NA. Molecular mechanism of proinflammatory cytokine-mediated squamous metaplasia in human corneal epithelial cells. Invest Ophthalmol Vis Sci. 2010;51(5):2466–75.
Article
PubMed
PubMed Central
Google Scholar
Tew SR, Hardingham TE. Regulation of SOX9 mRNA in human articular chondrocytes involving p38 MAPK activation and mRNA stabilization. J Biol Chem. 2006;281(51):39471–9.
Article
CAS
PubMed
Google Scholar
Zhang R, Murakami S, Coustry F, Wang Y, Crombrugghe B. Constitutive activation of MKK6 in chondrocytes of transgenic mice inhibits proliferation and delays endochondral bone formation. Proc Natl Acad Sci. 2006;103:352–70.
Article
Google Scholar
Akiyama H, Chaboissier M-C, Martin JF, Schedl A, 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;16:2813–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seymour PA, Freude KK, Tran MN, Mayes EE, Jensen J, Kist R, Scherer G, Sander M. SOX9 is required for maintenance of the pancreatic progenitor cell pool. Proc Natl Acad Sci. 2007;104(6):1865–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Acharya M, Lingenfelter DJ, Huang L, Gage PJ, Walter MA. Human PRKC apoptosis WT1 regulator is a novel PITX2-interacting protein that regulates PITX2 transcriptional activity in ocular cells. J Biol Chem. 2009;284(50):34829–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Toro R, Saadi I, Kuburas A, Nemer M, Russo AF. Cell-specific activation of the atrial natriuretic factor promoter by PITX2 and MEF2A. J Biol Chem. 2004;279(50):52087–94.
Article
CAS
PubMed
Google Scholar
Li C-S, Chae S-C, Lee J-H, Zhang Q, Chung H-T. Identification of single nucleotide polymorphisms in FOXJ1 and their association with allergic rhinitis. J Hum Genet. 2006;51(4):292–7.
Article
CAS
PubMed
Google Scholar
Gottardi AD, Dumonceau J-M, Bruttin F, Vonlaufen A, Morard I, Spahr L, Rubbia-Brandt L, Frossard J-L, Dinjens WN, Rabinovitch PS, et al. Expression of the bile acid receptor FXR in Barrett’s esophagus and enhancement of apoptosis by guggulsterone in vitro. Mol Cancer. 2006;5(48):48.
Article
PubMed
PubMed Central
Google Scholar
Fujino T, Murakami K, Ozawa I, Minegishi Y, Kashimura R, Akita T, Saitou S, Atsumi T, Sato T, Ando K, et al. Hypoxia downregulates farnesoid X receptor via a hypoxia-inducible factor-independent but p38 mitogen-activated protein kinase-dependent pathway. FEBS J. 2009;276(5):1319–32.
Article
CAS
PubMed
Google Scholar
Desbiens KM, Deschesnes RG, Labrie MM, Desfosses Y, Lambert H, Landry J, Bellmann AK. c-Myc potentiates the mitochondrial pathway of apoptosis by acting upstream of apoptosis signal-regulating kinase 1 (Ask1) in the p38 signalling cascade. Biochem J. 2003;372:631–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shuai K, Liu B. Regulation of JAK-STAT signalling in the immune system. Nat Rev Immunol. 2003;3(11):900–11.
Article
CAS
PubMed
Google Scholar