ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II () includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks.

[1]  S. Kim,et al.  ABFs, a Family of ABA-responsive Element Binding Factors* , 2000, The Journal of Biological Chemistry.

[2]  Andreas Schaller,et al.  Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family , 2005, PLoS Comput. Biol..

[3]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..

[4]  Yasukazu Nakamura,et al.  Distinctive features of plant organs characterized by global analysis of gene expression in Arabidopsis. , 2004, DNA research : an international journal for rapid publication of reports on genes and genomes.

[5]  Kazuo Shinozaki,et al.  A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. , 2004, The Plant journal : for cell and molecular biology.

[6]  S. Rhee,et al.  Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1 , 2004, Plant Physiology.

[7]  P. Reymond,et al.  Differential Gene Expression in Response to Mechanical Wounding and Insect Feeding in Arabidopsis , 2000, Plant Cell.

[8]  E. Grotewold,et al.  Genome wide analysis of Arabidopsis core promoters , 2005, BMC Genomics.

[9]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[10]  Chintalapati Janaki,et al.  Motif detection in Arabidopsis: Correlation with gene expression data , 2004, Silico Biol..

[11]  J E Mullet,et al.  A chloroplast lipoxygenase is required for wound-induced jasmonic acid accumulation in Arabidopsis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[12]  P. Zimmermann,et al.  Gene-expression analysis and network discovery using Genevestigator. , 2005, Trends in plant science.

[13]  Staffan Persson,et al.  Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[15]  Björn Usadel,et al.  CSB.DB: a comprehensive systems-biology database , 2004, Bioinform..

[16]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[17]  Junji Takabayashi,et al.  Functional identification of AtTPS03 as (E)-β-ocimene synthase: a monoterpene synthase catalyzing jasmonate- and wound-induced volatile formation in Arabidopsis thaliana , 2003, Planta.

[18]  Nick James,et al.  NASCArrays: a repository for microarray data generated by NASC's transcriptomics service , 2004, Nucleic Acids Res..

[19]  Thomas Altmann,et al.  Identification of brassinosteroid-related genes by means of transcript co-response analyses , 2005, Nucleic acids research.

[20]  John W. Pinney,et al.  Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis , 2006, Nucleic Acids Res..

[21]  Paul Horton,et al.  PROTEIN SUBCELLULAR LOCALIZATION PREDICTION WITH WOLF PSORT , 2005 .

[22]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[24]  C. Gachon,et al.  Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications , 2005, Plant Molecular Biology.

[25]  Saranyan K. Palaniswamy,et al.  AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks1[W][OA] , 2006, Plant Physiology.

[26]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[27]  Jacques Rougemont,et al.  DNA microarray data and contextual analysis of correlation graphs , 2003, BMC Bioinformatics.

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

[29]  R. Solano,et al.  JASMONATE-INSENSITIVE1 Encodes a MYC Transcription Factor Essential to Discriminate between Different Jasmonate-Regulated Defense Responses in Arabidopsis , 2004, The Plant Cell Online.

[30]  Weixiong Zhang,et al.  Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana , 2005, Bioinform..

[31]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[32]  Kazuo Shinozaki,et al.  Isolation and Functional Analysis of Arabidopsis Stress-Inducible NAC Transcription Factors That Bind to a Drought-Responsive cis-Element in the early responsive to dehydration stress 1 Promoterw⃞ , 2004, The Plant Cell Online.

[33]  R. Ferl,et al.  Transcription factor veracity: is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh? , 1996, The Plant cell.

[34]  Kazuki Saito,et al.  A New Member of Plant CS-lyases , 2003, The Journal of Biological Chemistry.

[35]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[36]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.

[37]  Feng Chen,et al.  An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. , 2003, The Plant journal : for cell and molecular biology.

[38]  Martin Schindler,et al.  AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome , 2004, Nucleic Acids Res..

[39]  Y. Choi,et al.  Jasmonic acid carboxyl methyltransferase: A key enzyme for jasmonate-regulated plant responses , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Y. Nakamura,et al.  Monitoring of methyl jasmonate-responsive genes in Arabidopsis by cDNA macroarray: self-activation of jasmonic acid biosynthesis and crosstalk with other phytohormone signaling pathways. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[41]  Peter D. Karp,et al.  MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research1[w] , 2005, Plant Physiology.

[42]  Hideyuki Suzuki,et al.  KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps1[w] , 2005, Plant Physiology.

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

[44]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..