ArticleBMC bioinformatics2008
SPIKE--a database, visualization and analysis tool of cellular signaling pathways.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins.Frontiers in immunology · 2018Article
- Protein-protein interaction analysis to identify biomarker networks for endometriosis.Experimental and therapeutic medicine · 2017Article
- NFPscanner: a webtool for knowledge-based deciphering of biomedical networks.BMC bioinformatics · 2017Article
- BRCA1/2 mutations perturb telomere biology: characterization of structural and functional abnormalities in vitro and in vivo.Oncotarget · 2016Article
- PAGER: constructing PAGs and new PAG-PAG relationships for network biology.Bioinformatics (Oxford, England) · 2015Article
- Extreme multifunctional proteins identified from a human protein interaction network.Nature communications · 2015Article
- PrOnto database : GO term functional dissimilarity inferred from biological data.Frontiers in genetics · 2015Article
- The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis.Frontiers in molecular biosciences · 2014Article
- Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data.Frontiers in genetics · 2014Article
- NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.BMC systems biology · 2013Article
- Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.PLoS computational biology · 2013Article
- E2F mediates enhanced alternative polyadenylation in proliferation.Genome biology · 2012Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The assimilation, visualization and interpretation of these data have become a major challenge in biological research, and once met, will greatly boost our ability to understand cell functioning on a systems level.
resultsTo cope with this challenge, we are developing the SPIKE knowledge-base of signaling pathways. SPIKE contains three main software components: 1) A database (DB) of biological signaling pathways. Carefully curated information from the literature and data from large public sources constitute distinct tiers of the DB. 2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. 3) An algorithmic inference engine that analyzes the networks for novel functional interplays between network components.SPIKE is designed and implemented as a community tool and therefore provides a user-friendly interface that allows registered users to upload data to SPIKE DB. Our vision is that the DB will be populated by a distributed and highly collaborative effort undertaken by multiple groups in the research community, where each group contributes data in its field of expertise.
conclusionThe integrated capabilities of SPIKE make it a powerful platform for the analysis of signaling networks and the integration of knowledge on such networks with omics data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.