BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
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...A notable example for this is the BioGPS Community Gene Portal System (53); this site provides ‘plugins’ through which users can connect any number of external websites into freely configurable screen layouts....
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...Second, partner websites can choose to embed the entire STRING website into their own pages (52,53), for example, using HTML inline frames (iframes)....
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2,512 citations
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...On the RNA level, the FANTOM consortium has been initiated to map the transcriptional space of the human genome and several gene expression atlases for RNA expression data have been launched, such as the original work to create a gene atlas by integrating mouse and human expression data from multiple tissues using micro arrays (7), the BioGPS portal with expression data from numerous sources (8), the repository ArrayExpress (9) and the RNA-Seq Atlas (10), with transcriptomics data based on deep sequencing from eleven normal human tissues....
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2,015 citations
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...BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources....
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...This section has the following subsections: a. mRNA expression graph: Provides normal tissue expression profiles for the gene, via experimental results from BioGPS (Wu et al., 2009), GTEx (Lonsdale et al., 2013[), Illumina Body Map, and SAGE....
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...Color-coded bars indicate the expression level in different tissues, as reported by BioGPS, GTex, and SAGE....
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1,771 citations
1,460 citations
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...This year, additional crossreferences to RSCB Protein Data Bank (34), Comparative Toxicogenomics Database (35), DockBlaster (36), BioGPS (37) and dbSNP (38) have been added to the protein pages....
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References
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"BioGPS: an extensible and customiza..." refers background in this paper
...The 'KEGG' layout shows biological pathways relevant to any particular gene of interest [15]....
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4,944 citations
"BioGPS: an extensible and customiza..." refers background in this paper
...In addition, there are a wide variety of gene annotation sites targeting more specific communities, including a database describing the targets of the transcription factor CREB [7], the Allen Brain Atlas showing high-resolution expression information by in situ hybridization in the mouse brain [ 8 ], and the TargetScan database for microRNA target prediction [9]....
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3,513 citations
"BioGPS: an extensible and customiza..." refers methods in this paper
...In addition, BioGPS hosts a gene expression plugin that displays reference expression patterns from the Gene Atlas data sets [6] and expression quantitative trait loci studies [20], as well as new data sets for an updated mouse Gene Atlas [GEO:GSE10246] [12] and exon array atlas [GEO:GSE15998]....
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...Moreover, we have included several reference datasets that have been extensively utilized in the microarray community through our SymAtlas website [6]....
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...In the case of BioGPS, the default gene annotation report focuses on our reference 'Gene Atlas' data sets, which show gene expression patterns from a diverse set of tissues and cell types [6,12,13]....
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...Other researchers may query reference Gene Atlas expression data using the SymAtlas web site [6]....
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2,394 citations
"BioGPS: an extensible and customiza..." refers methods in this paper
...visit the STRING database for protein interaction data [5]....
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