GATE
GATE is a software system used to analyze time-series expression data. It creates cluster files from time-series data for visualization as movies. It uses prior knowledge interaction networks and gene-lists libraries for identification of biological themes identified using the clustering analysis. 
URL: http://amp.pharm.mssm.edu/maayan-lab/gate.htm
Lists2Networks
Lists2Networks is a web-based software system used to analyze lists of mammalian genes. It creates a similarity matrix for many uploaded lists and compares the resultant lists to libraries of gene-lists from different categories. Users can create networks of lists and expand lists with prior knowledge networks such as protein-protein interactions, co-expression or co-annotation networks.
URL: http://www.lists2networks.org
Presynaptome: Network of protein-protein interactions within the synapse
Literature-based protein-protein interactions extracted from low-throughput experimental studies reporting interactions in mammalian presynaptic nerve terminals.
URL: http://amp.pharm.mssm.edu/presynaptome/
Neuronal Signalome
Literature-based cell signaling interactions extracted from literature describing components and interactions in mammalian neurons. This dataset was used in the paper (Ma'ayan et al. published in Science Aug. 12 2005).
Adhesome
Literature-based protein-protein interaction network extracted from publications describing functional interactions in adhesion complexes of mammalian cells.
iScMid
Literature-based protein-protein and gene-regulatory interactions extracted from publication describing interactions in mouse and human embryonic stem cells.
URL: http://amp.pharm.mssm.edu/iscmid
KEA
Kinase-substrate interactions collected from several databases collecting literature-based kinase-substrate interactions from experimental studies of mammalian cells.
URL: http://amp.pharm.mssm.edu/lib/kea.jsp
Genes2Networks
Protein-protein interactions collected from several databases collecting literature-based protein-protein interactions from experimental studies of mammalian cells.
URL: http://actin.pharm.mssm.edu/genes2networks
PathwayGenerator
Automatically generated pathways from receptors to effectors created using the neuronal signalome.
Files for download: A collection of Sig Files, and OWL Files (BioPAX2, BioPAX3) created from the Neuronal Signalome.
URL: http://amp.pharm.mssm.edu/maayan-lab/pg/
Cycles Study
Six biological directed networks of different types and three man-made directed networks of different types used to the analysis of large directed cycles.
URL: http://www.pnas.org/content/105/49/19235/suppl/DCSupplemental
Neuro2A differentiation by Galphai/o pathway on Science Signaling
Cell signaling pathways that traces downstream signaling pathways from Gi/o-coupled GPCRs to key protein kinases and key transcription factors involved in neuronal differentiation. Components in the Science Signaling Connections Map are linked to Nature Molecule Pages.
URL: http://stke.sciencemag.org/cgi/content/abstract/2/54/cm1
DOQCS
A repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.
Membrane Diffusion Coefficients
Partial Listing of diffusion coeffficients of integral membrane proteins provided by Suzanne Scarlata, Ph.D., SBCNY Investigator.
Files for download: Membrane Diffusion Coefficients TableURL: membrane_diffusion_coefficients.htm