title: ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses.
abstract: Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org.
authors.affiliation: RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan.
authors.forename: Kei
authors.initials: K
authors.lastname: Iida
authors.forename: Shuji
authors.initials: S
authors.lastname: Kawaguchi
authors.forename: Norio
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Manabu
authors.initials: M
authors.lastname: Ishii
authors.forename: Erimi
authors.initials: E
authors.lastname: Harada
authors.forename: Kousuke
authors.initials: K
authors.lastname: Hanada
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsui
authors.forename: Masanori
authors.initials: M
authors.lastname: Okamoto
authors.forename: Junko
authors.initials: J
authors.lastname: Ishida
authors.forename: Maho
authors.initials: M
authors.lastname: Tanaka
authors.forename: Taeko
authors.initials: T
authors.lastname: Morosawa
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D030541:Databases, Genetic; D005091:Exons; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D015233:Models, Statistical; D017422:Sequence Analysis, DNA / Q000379:methods; D013329:Structure-Activity Relationship; D049490:Systems Biology; D014584:User-Computer Interface