OryzaExpress

[…] ate genes from the already existing information such as the expression microarray data available in the public domain. In rice, using the microarray data, several publically accessible databases like OryzaExpress ([], http://plantomics.mind.meiji.ac.jp/OryzaExpress/ ), RicePLEX ([], http://www.plexdb.org/plex.php?database=Rice ), Rice Oligonucleotide Array database (ROAD) [], RiceSRTFDB ([], http: […]

[…] bserved if two or more unique peptides were measured for it across all iTRAQ labeled replicates. The ID of identified proteins was converted to Rice Genome Annotation Project ID with the converter at OryzaExpress: http://bioinf.mind.meiji.ac.jp/OryzaExpress/ID_converter.php. […]

[…] tp://www.ricearray.org/matrix.search.shtml), RiceXpro (http://ricexpro.dna.affrc.go.jp/), RiceGE, PLEXdb (http:// www.plexdb.org/plex.php?database=Rice), Oryza express (http://bioinf.mind.meiji.ac.jp/OryzaExpress/, Rise array net (http://www.ggbio.com/arraynet/), RED (http:// cdna02. dna.affrc.go.jp/RED/) NGS RGAP (http://rice.plant biology.msu.edu/expression.shtml), and UniVio (http://univio.psc. […]

[…] based co-expression applications, for example ATTED-II (, ), AraNet (), Expression Angler of the Bio-Array Resource (BAR; ), CressExpress (), CSB.DB (), KappaViewer (), GeneCAT (), Genevestigator (), OryzaExpress (), and VirtualPlant () have been developed (Table ).One of the best examples of co-expression analysis in Arabidopsis is cellulose synthase (CESA) genes in the secondary cell wall metabo […]

[…] explore gene expressions across a wide variety of biological contexts for rice and other species, but it is commercial and not completely publicly available (Hruz et al.[]). Other databases including OryzaExpress (Hamada et al.[]), RicePLEX within the Plant Expression Database (PLEXdb) (Dash et al.[]), Bio-Array Resource for Plant Biology (BAR) (Toufighi et al.[]) and Yale Virtual Center for Cellu […]

[…] mple, the node graph-based network visualization of co-expressed genes has been widely used in various plant species and has been implemented in web-accessible information resources such as ATTED-II, OryzaExpress and PlaNet (, , ). SeedNet and SCoPNet, at The Virtual Seed Web Resource (http://vseed.nottingham.ac.uk/), are genome-wide network models of transcriptional interactions in dormant and ge […]