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http://apps.cytoscape.org/apps/jepetto

A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.

Proper citation: JEPETTO (RRID:SCR_005909) Copy   

•   Source: SciCrunch Registry

http://www.droidb.org

A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available.

Proper citation: DroID - Drosophila Interactions Database (RRID:SCR_006634) Copy   

•   Source: SciCrunch Registry

https://jeonslab.snu.ac.kr/publication/trip-database-2-0-a-manually-curated-information-hub-for-accessing-trp-channel-interaction-network/

A manually curated database of protein-protein interactions (PPIs) for mammalian transient receptor potential (TRP) channels. The detailed summary of PPI data, fits into 4 categories: screening, validation, characterization, and functional consequence. These categorizations give answers for four basic questions about PPIs: how to identify PPIs (screening); how to confirm PPIs (validation); what are biochemical properties of PPIs (characterization); what are biological meaning of PPIs (functional consequence). Users can find in-depth information specified in the literature on relevant analytical methods, gene constructs, and cell/tissue types. The database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases.

Proper citation: TRIP Database (RRID:SCR_002058) Copy   

•   Source: SciCrunch Registry

http://www.coryneregnet.de

Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.

Proper citation: CoryneRegNet (RRID:SCR_002255) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/categoryCompare.html

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Proper citation: categoryCompare (RRID:SCR_001223) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/esb/PiNGO/

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: PiNGO (RRID:SCR_000692) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/cytospade

Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

Proper citation: CytoSPADE (RRID:SCR_001457) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://www.thebiogrid.org/

Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

http://www.altanalyze.org/

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

Proper citation: AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) Copy   

•   Source: SciCrunch Registry

http://www.imexconsortium.org/

Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.

Proper citation: IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) Copy   

•   Source: SciCrunch Registry