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The gene viewer can be accessed via the following URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html The official gene symbol as provided by the HUGO Gene Nomenclature Committee HGNCC) (14) is used as the unique identifier for reference gene documents.
We carried out a survey of the extent of homopolymer tract over-representation (enrichment) and over-proportional length distribution (above expected length) primarily in the single gene documents, but including some whole chromosomes of 27 eukaryotics across the (G+C)% composition range from 20 – 60%.
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There are two forms of this gene documented in a variety of species [110]: an intracellular and an extracellular form [111].
Each gene document was constructed by concatenation of all titles and abstracts of the Medline citations cross-referenced in the mouse, rat and human Entrez Gene entries as of 2007.
The absence of any change in the expression of chlorophyll biosynthesis genes documents that the expression of the carotenoid and chlorophyll genes can be regulated independently, at least in root tissue.
All titles and abstracts of the Medline citations cross-referenced in the mouse, rat and human Entrez Gene entries as of 2010 were concatenated to construct gene-documents and gene-gene similarity scores were calculated by LSI, as previously described [ 39, 40, 42].
There are 21 genes documented to be directly regulated genes by DosR [ 14].
First, yeast is the only organism which has more than 206000 TF-gene documented regulation data available.
To associate genes in Gw with documents in the corpus, we rely on a method that detects all abstracts mentioning a given gene and scores the occurrence based on syntactic and linguistic features such as place and frequency of occurrence resulting in a relevancy score for each gene-document pair [Phoebe Roberts, personal communication on LitMS gene-document index tool].
In the current study, about 2% of litchi unigenes induced by shading were found to be related to photosynthesis, and only 28% of the genes documented were repressed.
In this study, we developed a novel method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data.
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