croco-cyto

Web service plug-in for CroCo: the Cross-Species Conservation of Context-Specific Network (transcription factor-target gene) repository
Many large data compendia on context-specific high-throughput genomic and regulatory data have been made available by international research consortia such as ENCODE, TCGA, and Epigenomics Roadmap. The use of these resources is impaired by the sheer size of the available big data and big metadata. Many of these context-specific data can be modeled as data derived regulatory networks (DDRNs) representing the complex and complicated interactions between transcription factors and target genes. The Cross-species Conservation framework (CroCo) provides a network-oriented view on the ENCODE regulatory data (CroCo network repository), convenient ways to access and browse networks and metadata, and a method to combine networks across compendia, experimental techniques and species (CroCo tool suite). DDRNs can be combined with additional information and networks derived from the literature, curated resources and computational predictions in order to allow detailed exploration and cross checking of regulatory interactions. Applications of the CroCo framework range from simple evidence look-up for user-defined regulatory interactions to the identification of conserved sub-networks in diverse cell-lines, conditions, or even species. CroCo adds an intuitive unifying view on the data from the ENCODE projects via a comprehensive repository of derived context-specific regulatory networks and enables flexible cross-context, cross-species and cross-compendia comparison by a basis set of analysis tools. ***Project web-site and users guide:*** [https://services.bio.ifi.lmu.de/croco-web/] ### Quick start * Select: File/Import/Network/Public database * Select: Data Source: croco-cyto * Insert the web-service URL: https://services.bio.ifi.lmu.de/croco-web/services/ * Click on: connect * Select network from the ### Demo video [![IMAGE ALT TEXT](http://img.youtube.com/vi/-3vOKkNUoEk/0.jpg)](http://www.youtube.com/watch?v=-3vOKkNUoEk "croco-cyto demonstration")

1.1

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.1

Released 11 Mar 2016

Works with Cytoscape 3.0

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