Running head: ATTED-II in 2014: Gene Coexpression Evaluation

[1]  Reza Salavati,et al.  Sequence-based prediction of protein-protein interactions by means of codon usage , 2008, Genome Biology.

[2]  N. Provart,et al.  BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. , 2012, The Plant journal : for cell and molecular biology.

[3]  Kiana Toufighi,et al.  The Botany Array Resource: E-northerns, Expression Angling, and Promoter Analyses , 2022 .

[4]  S. Robinson,et al.  Food Security: The Challenge of Feeding 9 Billion People , 2010, Science.

[5]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[6]  Nori Kurata,et al.  OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice , 2010, Plant & cell physiology.

[7]  Rainer Spang,et al.  Similarities of Ordered Gene Lists , 2006, J. Bioinform. Comput. Biol..

[8]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[9]  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 .

[10]  Hailin Chen,et al.  STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data , 2009, BMC Bioinformatics.

[11]  Yoshihiro Kawahara,et al.  Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics , 2013, Plant & cell physiology.

[12]  Staffan Persson,et al.  Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. , 2009, Plant, cell & environment.

[13]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[14]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[15]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[16]  Kengo Kinoshita,et al.  Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis , 2009, Bioinform..

[17]  Staffan Persson,et al.  GeneCAT—novel webtools that combine BLAST and co-expression analyses , 2008, Nucleic Acids Res..

[18]  Maria Keays,et al.  ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..

[19]  B. Usadel,et al.  PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA] , 2011, Plant Cell.

[20]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[21]  Kengo Kinoshita,et al.  ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants , 2011, Plant & cell physiology.

[22]  Hideyuki Suzuki,et al.  CoP: a database for characterizing co-expressed gene modules with biological information in plants , 2010, Bioinform..

[23]  Lorenzo Farina,et al.  The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana , 2012, Genetics.

[24]  Kengo Kinoshita,et al.  Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways , 2010, Journal of Plant Research.

[25]  Martijn A. Huynen,et al.  Conserved co-expression for candidate disease gene prioritization , 2008, BMC Bioinformatics.

[26]  Yoshiyuki Ogata,et al.  Approaches for extracting practical information from gene co-expression networks in plant biology. , 2007, Plant & cell physiology.

[27]  Andrew H. Paterson,et al.  Synteny and Collinearity in Plant Genomes , 2008, Science.

[28]  Kengo Kinoshita,et al.  ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis , 2006, Nucleic Acids Res..

[29]  Arnold J Levine,et al.  Tissue-specific codon usage and the expression of human genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[31]  Reza Salavati,et al.  Universal function-specificity of codon usage , 2009, Nucleic acids research.

[32]  Kengo Kinoshita,et al.  COXPRESdb: a database to compare gene coexpression in seven model animals , 2010, Nucleic Acids Res..

[33]  K. Kinoshita,et al.  Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[34]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[35]  D. McClish Analyzing a Portion of the ROC Curve , 1989, Medical decision making : an international journal of the Society for Medical Decision Making.

[36]  Kengo Kinoshita,et al.  COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals , 2012, Nucleic Acids Res..

[37]  Klaas Vandepoele,et al.  Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice1[W] , 2011, Plant Physiology.

[38]  Kengo Kinoshita,et al.  ATTED-II provides coexpressed gene networks for Arabidopsis , 2008, Nucleic Acids Res..

[39]  W. C. Yim,et al.  PLANEX: the plant co-expression database , 2013, BMC Plant Biology.