COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species.

[1]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[2]  George A Wells,et al.  The Genome-Wide Association Study—A New Era for Common Polygenic Disorders , 2010, Journal of cardiovascular translational research.

[3]  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.

[4]  Xiaoqi Zheng,et al.  Large cliques in Arabidopsis gene coexpression network and motif discovery. , 2011, Journal of plant physiology.

[5]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[6]  Hitoshi Nomura,et al.  ASCL1-coexpression profiling but not single gene expression profiling defines lung adenocarcinomas of neuroendocrine nature with poor prognosis. , 2012, Lung cancer.

[7]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[8]  A. Loraine,et al.  Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm1[W] , 2009, Plant Physiology.

[9]  Robert J Gillies,et al.  Gene expression profiling-based identification of cell-surface targets for developing multimeric ligands in pancreatic cancer , 2008, Molecular Cancer Therapeutics.

[10]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[11]  Gary D. Bader,et al.  Cytoscape Web: an interactive web-based network browser , 2010, Bioinform..

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

[13]  Michele Caselle,et al.  Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes , 2001, BMC Bioinformatics.

[14]  David J. Arenillas,et al.  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..

[15]  Rajeev Motwani,et al.  The PageRank Citation Ranking : Bringing Order to the Web , 1999, WWW 1999.

[16]  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.

[17]  Xinyu Liu,et al.  SNPxGE2: a database for human SNP-coexpression associations , 2012, Bioinform..

[18]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[19]  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.

[20]  Peter Widmayer,et al.  Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes , 2008, Adv. Bioinformatics.

[21]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

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

[23]  Kenta Nakai,et al.  DBTSS: DataBase of Transcriptional Start Sites progress report in 2012 , 2011, Nucleic Acids Res..

[24]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

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

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

[27]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[28]  Kengo Kinoshita,et al.  COXPRESdb: a database of coexpressed gene networks in mammals , 2007, Nucleic Acids Res..

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

[30]  Ibrahim Emam,et al.  ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments , 2010, Nucleic Acids Res..

[31]  Toshihisa Takagi,et al.  Interactive, multiscale navigation of large and complicated biological networks , 2011, Bioinform..

[32]  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.

[33]  María Martín,et al.  The Gene Ontology: enhancements for 2011 , 2011, Nucleic Acids Res..