Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.
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Pierre Geurts | Stein Aerts | Gert Hulselmans | Valerie Christiaens | Kristofer Davie | Vân Anh Huynh-Thu | Delphine Potier | P. Geurts | S. Aerts | V. A. Huynh-Thu | Kristofer Davie | Duygu Koldere | V. Christiaens | Gert Hulselmans | Delphine Potier | Marina Naval Sanchez | Lotte Haagen | A. Çelik | Marina Naval Sanchez | Arzu Celik | Lotte Haagen | Duygu Koldere | K. Davie
[1] William Stafford Noble,et al. Analysis of strain and regional variation in gene expression in mouse brain , 2001, Genome Biology.
[2] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[3] A. Regev,et al. Dynamic regulatory network controlling Th17 cell differentiation , 2013, Nature.
[4] Zohar Yakhini,et al. Discovering Motifs in Ranked Lists of DNA Sequences , 2007, PLoS Comput. Biol..
[5] Ken W. Y. Cho,et al. Schnurri transcription factors from Drosophila and vertebrates can mediate Bmp signaling through a phylogenetically conserved mechanism , 2006, Development.
[6] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[7] Kathryn L. Pepple,et al. Two-step selection of a single R8 photoreceptor: a bistable loop between senseless and rough locks in R8 fate , 2008, Development.
[8] Laura Ponting,et al. FlyBase 102—advanced approaches to interrogating FlyBase , 2013, Nucleic Acids Res..
[9] Fernando Casares,et al. Size matters: the contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network. , 2010, Developmental biology.
[10] Stein Aerts,et al. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections , 2014, PLoS Comput. Biol..
[11] Fangxue Sherry He,et al. Systematic identification of mammalian regulatory motifs' target genes and functions , 2008, Nature Methods.
[12] L. Hood,et al. A Genomic Regulatory Network for Development , 2002, Science.
[13] Gos Micklem,et al. Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode , 2022 .
[14] M. Mckeown,et al. Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors , 2004, Development.
[15] Yves Van de Peer,et al. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data , 2010, Bioinform..
[16] D. di Bernardo,et al. Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation , 2012, Nucleic acids research.
[17] N. Fuse,et al. Diploidy of Drosophila imaginal cells is maintained by a transcriptional repressor encoded by escargot. , 1994, Genes & development.
[18] S. Mangan,et al. Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[19] C. Myers,et al. A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions , 2016, Molecular systems biology.
[20] G. Mardon,et al. Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. , 2006, Genome research.
[21] J. Kumar. The molecular circuitry governing retinal determination. , 2009, Biochimica et biophysica acta.
[22] Daniel Chourrout,et al. Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.
[23] Huda Y Zoghbi,et al. Drosophila atonal Fully Rescues the Phenotype of Math1 Null Mice New Functions Evolve in New Cellular Contexts , 2002, Current Biology.
[24] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[25] G. Mardon,et al. senseless Repression of rough Is Required for R8 Photoreceptor Differentiation in the Developing Drosophila Eye , 2001, Neuron.
[26] Stein Aerts,et al. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions , 2013, Genome research.
[27] Franck Pichaud,et al. Combinatorial control of Drosophila eye development by eyeless, homothorax, and teashirt. , 2002, Genes & development.
[28] Gerald M. Rubin,et al. The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells , 1989, Nature.
[29] Richard Bonneau,et al. A Validated Regulatory Network for Th17 Cell Specification , 2012, Cell.
[30] Duc-Hau Le,et al. A coherent feedforward loop design principle to sustain robustness of biological networks , 2013, Bioinform..
[31] Sarah A. Teichmann,et al. FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database , 2009, Nucleic Acids Res..
[32] D. J. McKay,et al. A common set of DNA regulatory elements shapes Drosophila appendages. , 2013, Developmental cell.
[33] James B. Brown,et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions , 2009, Genome Biology.
[34] U. Banerjee,et al. In vivo analysis of a developmental circuit for direct transcriptional activation and repression in the same cell by a Runx protein. , 2003, Genes & development.
[35] E. Furlong,et al. A core transcriptional network for early mesoderm development in Drosophila melanogaster. , 2007, Genes & development.
[36] David Botstein,et al. GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..
[37] S. Aerts,et al. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules , 2012, Nucleic acids research.
[38] Gerald M Rubin,et al. A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. , 2012, Cell reports.
[39] Thomas Whitington,et al. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.
[40] K. White,et al. Analysis of the eye developmental pathway in Drosophila using DNA microarrays , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[41] Adam A. Margolin,et al. Reverse engineering of regulatory networks in human B cells , 2005, Nature Genetics.
[42] E. Birney,et al. A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History , 2012, Cell.
[43] Stein Aerts,et al. Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification , 2010, PLoS biology.
[44] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[45] David Z. Chen,et al. Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.
[46] Mehdi M. Kashani,et al. Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors , 2014, Cell.
[47] Alain Guénoche,et al. Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters , 2013, Biosyst..
[48] Julie H. Simpson,et al. A GAL4-driver line resource for Drosophila neurobiology. , 2012, Cell reports.
[49] Panayiotis V. Benos,et al. STAMP: a web tool for exploring DNA-binding motif similarities , 2007, Nucleic Acids Res..
[50] G. Stormo,et al. Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites , 2008, Cell.
[51] N. Friedman,et al. Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis , 2011, Cell.
[52] P. Geurts,et al. Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.
[53] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[54] Bassem A. Hassan,et al. Transcriptional control of cell fate specification: lessons from the fly retina. , 2012, Current topics in developmental biology.
[55] Utpal Banerjee,et al. A transcriptional chain linking eye specification to terminal determination of cone cells in the Drosophila eye. , 2003, Developmental biology.
[56] Diogo M. Camacho,et al. Wisdom of crowds for robust gene network inference , 2012, Nature Methods.
[57] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[58] Kate B. Cook,et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.
[59] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[60] Felicia S. L. Ng,et al. Key regulators control distinct transcriptional programmes in blood progenitor and mast cells , 2014, The EMBO journal.
[61] Christian A. Grove,et al. A Gene-Centered C. elegans Protein-DNA Interaction Network , 2006, Cell.
[62] Rakesh K. Mishra,et al. Efficient and Specific Targeting of Polycomb Group Proteins Requires Cooperative Interaction between Grainyhead and Pleiohomeotic , 2006, Molecular and Cellular Biology.
[63] S. Shen-Orr,et al. Network motifs: simple building blocks of complex networks. , 2002, Science.