VistaClara: an expression browser plug-in for Cytoscape
نویسندگان
چکیده
SUMMARY VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular in gene-expression analysis. This extended browser permits a variety of display options and interactions not currently available in Cytoscape. AVAILABILITY http://chianti.ucsd.edu/cyto_web/plugins/index.php.
منابع مشابه
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
SUMMARY Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs. DvD allows users to compare drug and ...
متن کاملGenoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
UNLABELLED Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources throu...
متن کاملCytoscape: a software environment for integrated models of biomolecular interaction networks.
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interac...
متن کاملCytoGTA: A cytoscape plugin for identifying discriminative subnetwork markers using a game theoretic approach
In recent years, analyzing genome-wide expression profiles to find genetic markers has received much attention as a challenging field of research aiming at unveiling biological mechanisms behind complex disorders. The identification of reliable and reproducible markers has lately been achieved by integrating genome-scale functional relationships and transcriptome datasets, and a number of algor...
متن کاملOmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data
SUMMARY OmicsAnalyzer is a Cytoscape plug-in for visual omics-based network analysis that (i) integrates hetero-omics data for one or more species; (ii) performs statistical tests on the integrated datasets; and (iii) visualizes results in a network context. AVAILABILITY Implemented in Java, OmicsAnalyzer runs with Cytoscape 2.6 and 2.7. Binaries, documentation and video walkthroughs are free...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 24 شماره
صفحات -
تاریخ انتشار 2008