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Using an expression signature specific to lung adenocarcinoma, a number of compounds from C-MAP analysis were identified for having negatively-correlated effects on expression of query signature.
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Some works have been carried out in the past years in order to design languages allowing the expression of queries involving preferences through the use of fuzzy predicates.
Compounds with negative connectivity scores, which imply a mode of action by the matched compounds to reverse the expression direction of query genes in lung adenocarcinoma, were recorded as potential therapeutic agents for lung adenocarcinoma.
Another method for compound target prediction involves comparing the gene expression profiles of query compounds with those of other compounds of known target proteins.
With respect to the web interface, the first aspect to consider is that the gene signature collection should be linked to both a gene search interface that retrieves differential expression information of query gene as well as a signature comparison interface that compares user-selected signatures to identify common genes for prioritization.
The search criteria model provides a 'detached' version of the popular Hibernate 2 Criteria API, which enables expression of complex query constraints.
Next, graph connectivity is further enriched by taking into account the pairwise differential changes in expression of the query genes for different conditions in the experiment.
Different options are proposed for the expression of the query results: Contents of either individual polyphenols or calculated total polyphenols in a given polyphenol class or subclass are given.
GEM-TREND was developed to retrieve gene expression data by comparing the gene-expression pattern of queries with those of gene expression data in a public database based on the nonparametric, rank-based pattern matching approach with the additional calculation of statistical significance and to provide network visualization.
All real-time PCR assays generated a single band of the expected size, and therefore accurately represented the expression of the queried gene.
The use of wild card (*, ?, '//', etc). in the path expressions of a query allows users to query documents whose structural information is not available.
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