Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

A new computational method uses gene expression databases and transcription factor binding specificities to describe regulatory elements in the Drosophila A/P patterning network in unprecedented detail.

[1]  D. W. Knowles,et al.  Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm , 2008, PLoS biology.

[2]  Saurabh Sinha,et al.  Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila , 2004, BMC Bioinformatics.

[3]  Tim Hui-Ming Huang,et al.  Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. , 2002, Genes & development.

[4]  David H. Sharp,et al.  Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene , 2006, Nature Genetics.

[5]  M. Levine,et al.  A systems view of Drosophila segmentation , 2008, Genome Biology.

[6]  G. Jiménez,et al.  Relief of gene repression by torso RTK signaling: role of capicua in Drosophila terminal and dorsoventral patterning. , 2000, Genes & development.

[7]  J. Mohler.  Genetic regulation of CNC expression in the pharnygeal primordia ofDrosophila blastoderm embryos , 1993, Roux's archives of developmental biology.

[8]  J. R. Rohlicek,et al.  Parameter estimation of dependence tree models using the EM algorithm , 1995, IEEE Signal Processing Letters.

[9]  M. Noyes,et al.  A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system , 2008, Nucleic acids research.

[10]  Steven M. Gallo,et al.  REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila , 2007, Nucleic Acids Res..

[11]  E. L. Lehmann,et al.  Theory of point estimation , 1950 .

[12]  Stein Aerts,et al.  Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes , 2007, PloS one.

[13]  Yoosik Kim,et al.  MAPK Substrate Competition Integrates Patterning Signals in the Drosophila Embryo , 2010, Current Biology.

[14]  Johannes Jaeger,et al.  Gene Circuit Analysis of the Terminal Gap Gene huckebein , 2009, PLoS Comput. Biol..

[15]  N. Patel,et al.  Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. , 1998, Development.

[16]  M. Biggin,et al.  Eve and ftz regulate a wide array of genes in blastoderm embryos: the selector homeoproteins directly or indirectly regulate most genes in Drosophila. , 1998, Development.

[17]  Ho-Ryun Chung,et al.  Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains , 2009, Proceedings of the National Academy of Sciences.

[18]  Hao Li,et al.  Regulatory element detection using correlation with expression (abstract only) , 2001, RECOMB.

[19]  J. Lengyel,et al.  The torso response element binds GAGA and NTF-1/Elf-1, and regulates tailless by relief of repression. , 1995, Genes & development.

[20]  Xiaoyu Chen,et al.  Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees , 2007, BMC Bioinformatics.

[21]  Colin N. Dewey,et al.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , 2007, Nature.

[22]  G. Rubin,et al.  Tools for neuroanatomy and neurogenetics in Drosophila , 2008, Proceedings of the National Academy of Sciences.

[23]  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.

[24]  David H. Sharp,et al.  Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation , 2009, PLoS biology.

[25]  J. Felsenstein.  Maximum-likelihood estimation of evolutionary trees from continuous characters. , 1973, American journal of human genetics.

[26]  W. Miller,et al.  Distinguishing regulatory DNA from neutral sites. , 2003, Genome research.

[27]  M. Levine,et al.  Shadow Enhancers as a Source of Evolutionary Novelty , 2008, Science.

[28]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[29]  Syr-yaung Lin,et al.  The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes , 1975, Cell.

[30]  E. Steingrímsson,et al.  bicoid and the terminal system activate tailless expression in the early Drosophila embryo. , 1992, Development.

[31]  G. Church,et al.  A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. , 2004, Genome research.

[32]  John Reinitz,et al.  A database for management of gene expression data in situ , 2004, Bioinform..

[33]  M Klingler,et al.  Two gap genes mediate maternal terminal pattern information in Drosophila. , 1990, Science.

[34]  S. Panchanathan,et al.  BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. , 2002, Genetics.

[35]  G. Stormo,et al.  Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites , 2008, Cell.

[36]  H. Akaike.  A new look at the statistical model identification , 1974 .

[37]  David A. Nix,et al.  Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila , 2006, PLoS Comput. Biol..

[38]  Leon Glass,et al.  Reverse Engineering the Gap Gene Network of Drosophila melanogaster , 2006, PLoS Comput. Biol..

[39]  Charless C. Fowlkes,et al.  A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm , 2008, Cell.

[40]  J. Fak,et al.  Transcriptional Control in the Segmentation Gene Network of Drosophila , 2004, PLoS biology.

[41]  Saurabh Sinha,et al.  A probabilistic method to detect regulatory modules , 2003, ISMB.

[42]  G. Rubin,et al.  Global analysis of patterns of gene expression during Drosophila embryogenesis , 2007, Genome Biology.

[43]  Casey M. Bergman,et al.  Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster , 2005, Bioinform..

[44]  David H. Sharp,et al.  Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster , 2004, Genetics.

[45]  J. B. Jaynes,et al.  Drosophila SAP18, a member of the Sin3/Rpd3 histone deacetylase complex, interacts with Bicoid and inhibits its activity , 2001, Development, Genes and Evolution.

[46]  Manolis Kellis,et al.  Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. , 2007, Genes & development.

[47]  B. Ren,et al.  An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome , 2009, PloS one.

[48]  Manolis Kellis,et al.  Reliable prediction of regulator targets using 12 Drosophila genomes. , 2007, Genome research.

[49]  E. Furlong,et al.  Combinatorial binding predicts spatio-temporal cis-regulatory activity , 2009, Nature.

[50]  J. Rodgers,et al.  Thirteen ways to look at the correlation coefficient , 1988 .

[51]  Martin C. Frith,et al.  Cluster-Buster: finding dense clusters of motifs in DNA sequences , 2003, Nucleic Acids Res..

[52]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[53]  L. Stevens,et al.  The Drosophila Embryonic Patterning Determinant Torsolike Is a Component of the Eggshell , 2003, Current Biology.

[54]  S. Salzberg,et al.  Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura , 2004, Genome Biology.

[55]  E. Segal,et al.  Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.

[56]  A. Tsirigos,et al.  Anterior-posterior positional information in the absence of a strong Bicoid gradient , 2009, Proceedings of the National Academy of Sciences.

[57]  Massimo Vergassola,et al.  Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo , 2002, BMC Bioinformatics.

[58]  A. Bagri,et al.  Salivary gland determination in Drosophila: a salivary-specific, fork head enhancer integrates spatial pattern and allows fork head autoregulation. , 2001, Developmental biology.

[59]  L. -. Wu,et al.  Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. , 1998, Development.

[60]  E. Davidson.  Genomic Regulatory Systems: Development and Evolution , 2005 .

[61]  H. Bussemaker,et al.  Regulatory element detection using correlation with expression , 2001, Nature Genetics.

[62]  Arend Sidow,et al.  Constructing a meaningful evolutionary average at the phylogenetic center of mass , 2007, BMC Bioinformatics.