Literature DB >> 16198288

Genomic regulatory networks and animal development.

Angelike Stathopoulos1, Michael Levine.   

Abstract

The synthesis of gene expression data and cis-regulatory analysis permits the elucidation of genomic regulatory networks. These networks provide a direct visualization of the functional interconnections among the regulatory genes and signaling components leading to cell-specific patterns of gene activity. Complex developmental processes are thereby illuminated in ways not revealed by the conventional analysis of individual genes. In this review, we describe emerging networks in several different model systems, and compare them with the gene regulatory network that controls dorsoventral patterning of the Drosophila embryo.

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Year:  2005        PMID: 16198288     DOI: 10.1016/j.devcel.2005.09.005

Source DB:  PubMed          Journal:  Dev Cell        ISSN: 1534-5807            Impact factor:   12.270


  108 in total

1.  An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells.

Authors:  Ipsita Banerjee; Spandan Maiti; Natesh Parashurama; Martin Yarmush
Journal:  Bioinformatics       Date:  2010-03-31       Impact factor: 6.937

2.  Cofactor-mediated restriction of GATA-1 chromatin occupancy coordinates lineage-specific gene expression.

Authors:  Timothy M Chlon; Louis C Doré; John D Crispino
Journal:  Mol Cell       Date:  2012-07-05       Impact factor: 17.970

3.  Differential Masking of Natural Genetic Variation by miR-9a in Drosophila.

Authors:  Justin J Cassidy; Alexander J Straughan; Richard W Carthew
Journal:  Genetics       Date:  2015-11-27       Impact factor: 4.562

4.  Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.

Authors:  Frédéric Biemar; David A Nix; Jessica Piel; Brant Peterson; Matthew Ronshaugen; Victor Sementchenko; Ian Bell; J Robert Manak; Michael S Levine
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-14       Impact factor: 11.205

Review 5.  Ciona intestinalis as a model for cardiac development.

Authors:  Brad Davidson
Journal:  Semin Cell Dev Biol       Date:  2006-12-20       Impact factor: 7.727

Review 6.  Enhancer identification through comparative genomics.

Authors:  Axel Visel; James Bristow; Len A Pennacchio
Journal:  Semin Cell Dev Biol       Date:  2007-01-05       Impact factor: 7.727

Review 7.  High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution.

Authors:  Meredith Howard-Ashby; Stefan C Materna; C Titus Brown; Qiang Tu; Paola Oliveri; R Andrew Cameron; Eric H Davidson
Journal:  Dev Biol       Date:  2006-10-18       Impact factor: 3.582

8.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Authors:  Alexander Stark; Michael F Lin; Pouya Kheradpour; Jakob S Pedersen; Leopold Parts; Joseph W Carlson; Madeline A Crosby; Matthew D Rasmussen; Sushmita Roy; Ameya N Deoras; J Graham Ruby; Julius Brennecke; Emily Hodges; Angie S Hinrichs; Anat Caspi; Benedict Paten; Seung-Won Park; Mira V Han; Morgan L Maeder; Benjamin J Polansky; Bryanne E Robson; Stein Aerts; Jacques van Helden; Bassem Hassan; Donald G Gilbert; Deborah A Eastman; Michael Rice; Michael Weir; Matthew W Hahn; Yongkyu Park; Colin N Dewey; Lior Pachter; W James Kent; David Haussler; Eric C Lai; David P Bartel; Gregory J Hannon; Thomas C Kaufman; Michael B Eisen; Andrew G Clark; Douglas Smith; Susan E Celniker; William M Gelbart; Manolis Kellis
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

9.  Between "design" and "bricolage": genetic networks, levels of selection, and adaptive evolution.

Authors:  Adam S Wilkins
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-09       Impact factor: 11.205

10.  Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.

Authors:  Lev G Nikolaev; Sergey B Akopov; Igor P Chernov; Eugene D Sverdlov
Journal:  Curr Genomics       Date:  2007-04       Impact factor: 2.236

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