Databases and Datasets

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.
PMID: 20709693 | PMCID: PMC2944209 | EndNote Citation

Files for download: Ivanova_Dppa4 timeseries.clu, Ivanova_Esrrb timeseries.clu, Ivanova_Nanog timeseries.clu, Ivanova_Oct4 timeseries.clu, Ivanova_Sox2 timeseries.clu, Ivanova_Tbx3 timeseries.clu, Ivanova_Tcl1 timeseries.clu, Lu_nanog_his.clu, Lu_nanog_mRNA.clu, Lu_nanog_nuclear_pro.clu, Lu_nanog_pol.clu

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.
PMID: 20152038 | PMCID: PMC2843617 | EndNote Citation | Biositemaps (RDF)

Files for download: ChIP.gmt, GO_BP.gmt, GO_CC.gmt, GO_MF.gmt, Kinase_Substrates.dat, Metabolites.gmt, OMIM_Disease_Genes.gmt, OMIM_Expanded.gmt, Pfam-InterPro-domains.gmt, Predicted_Promoter_Sites.gmt, Protein_Interaction_Hubs50.gmt, WikiPathways.gmt, chromosome.gmt, miRNA.gmt

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.
PMID: 19562802 | EndNote Citation | Biositemaps (RDF)

Files for download: presynaptome.txt, presynaptome_biopax2.owl

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).
PMID: 16099987 | EndNote Citation

Files for download: neuronal_signalome.owl, neuronal_signalome.txt

URL: Supplementary Materials

Adhesome
Literature-based protein-protein interaction network extracted from publications describing functional interactions in adhesion complexes of mammalian cells. PMID: 17671451 | EndNote Citation | Biositemaps (RDF)

Files for download: fa sif, fa.sig, fa.txt, fa.net, fa.avis

URL: http://www.adhesome.org

iScMid
Literature-based protein-protein and gene-regulatory interactions extracted from publication describing interactions in mouse and human embryonic stem cells.
PMID: 19738627 | EndNote Citation | Biositemaps (RDF)

Files for download: iscmid_chip.csv, literature.txt

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.
PMID: 19176546 | EndNote Citation | Biositemaps (RDF)

Files for download: kea.sig, kinome.sig

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.
PMID: 17916244 | EndNote Citation | Biositemaps (RDF)

Files for download: BIND.sig, DIP.sig, HPRD.sig, IntAct.sig, MINT.sig, SAVI.sig, Stelzl.sig, adhesome.sig, biogrid.sig, figeys.sig, hiv.sig, kea.sig, kegg.sig, mips.sig, pdzbase.sig, phosphoelm.sig, ppid.sig, presynaptome.sig, reactome.sig, tf_y2h_human.sig, tf_y2h_mouse.sig, vidal.sig

URL: http://actin.pharm.mssm.edu/genes2networks

PathwayGenerator
Automatically generated pathways from receptors to effectors created using the neuronal signalome.
PMID: 16099987 | EndNote Citation | Biositemaps (RDF)

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.
PMID: 19033453 | EndNote Citation

Files for download: brain.sig, ecoli.sig, electrical.sig, faa.sig fixed_neuron.sig, foodweb.sig, signaling.sig, tracert.sig, yeast.sig

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.
PMID: 19155528 | EndNote Citation

Files for download: Neuro2A_pathway_for_Flash_viewer.xml

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.
PMID: 12584128 | EndNote Citation | Biositemaps (RDF)

URL: http://doqcs.ncbs.res.in


Membrane Diffusion Coefficients
Partial Listing of diffusion coeffficients of integral membrane proteins provided by Suzanne Scarlata, PhD, SBCNY Investigator.

Files for download: Membrane Diffusion Coefficients Table

URL: membrane_diffusion_coefficients.htm

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