Software

Kinase Enrichment Analysis (KEA) is a web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. The system draws from several available kinase-substrate databases to computes kinase enrichment probability based on the distribution of kinase-substrate proportions in the background kinase-substrate database compared with kinases found to be associated with an input list of genes/proteins.
Website: KEA web-interface | KEA command-line version | paper

Genes2Networks is a command-line software tool that can be used to place lists of mammalian genes in the context of a background mammalian signalome and interactome networks. The input to the program is a list of human Entrez Gene gene symbols and background networks in SIG format, while the output includes: (a) all identified interactions for the genes/proteins, (b) a subnetwork connecting the genes/proteins using intermediate components that are used to connect the genes, (c) ranking of the specificity of intermediate components to interact with the list of genes/proteins.
Web site: Genes2Networks command line version | Genes2Networks web interface | paper

AVIS AJAX Viewer for Signaling Networks is a visualization tool for viewing and sharing intracellular signaling, gene regulation and protein interaction networks. AVIS is implemented as an AJAX enabled syndicated Google gadget. It allows any webpage to render an image from a text file representation of signaling, gene regulatory, or protein interaction networks.
Web site: AVIS | paper

SNAVI (Signaling Networks Analysis and Visualization) is a Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software.
Web site: SNAVI | paper

PubMed Alert Me! is a software utility that allows users to enter a list of PubMed queries. Once a list of queries is configured, the program runs either daily or weekly. It searches PubMed and if it finds new matching published papers, the program sends an e-mail notification with a list of links to the new articles.
Web site: PubMed Alert Me! | paper

SequenceViewer is a software system that includes two bioinformatics tools: DNAViewer and RepeatsViewer. These Windows based computer programs create graphical images from text DNA sequences in FASTA format. The images created by the tools can help researchers identify repeating patterns, letter concentrations in different regions of DNA and possibly give clues about DNA physical structure as well as identifying novel promoter binding sites.
Web site: SequenceViewer

Datasets and Systems

Network Datasets for Download: in SIG file format

Neuronal Signaling Network - A massive literature search was applied to develop a large-scale mammalian neuronal cell signaling network. This network integrate cell signaling pathways specific to mammalian neurons. The network was analyzed for topological properties in the in this article published in Science. Additional information can be viewed at: http://www.mssm.edu/labs/iyengar/resources/networks/signaling_networks.shtml. The most recent version of this network is available at: http://amp.pharm.mssm.edu/SAVI.txt.

Adhesome - A comprehensive literature derived biochemical network was developed in collaboration with Benny Geiger's Lab. The network is made of known interactions and cellular components composing the focal adhesion complex in mammalian cells. The Adhesome web-site provides a reference and supporting materials to the analysis published in Nature Cell Biology.

PathwayGenerator - A web-based interface that allows users to retrieve automatically generated pathways by selecting extra-cellular ligands as source nodes/molecules and selecting a target node that belongs to a cellular machine (i.e. transcription factor). The program searches for all possible pathways that can be reached from the source to the target in the least number of steps and presents a connection maps similar to the familiar connection maps published on STKE.