Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Reactome BioMart provides biologists and bioinformaticians with a single web interface for performing simple or elaborate queries of the Reactome database, aggregating data from different sources and providing an opportunity to integrate experimental and computational results with information relating to biological pathways. Database URL: http://www.reactome.org.
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http://dx.doi.org/10.1093/database/bar031 | DOI Listing |
Bioinform Adv
October 2024
Institute for Applied Mathematics (IAC) "Mauro Picone", National Research Council (CNR), Rome 00185, Italy.
Summary: We present , an R package able to perform , , and data extraction from Systems Biology Markup Language (SBML) documents (up to Level 3) in tabular data structures (i.e. R dataframes) to easily access and handle the richness of the biological information.
View Article and Find Full Text PDFMed Oncol
January 2022
Department of Molecular Biology and Genetics, Science Faculty, Erzurum Technical University, Erzurum, 25050, Turkey.
Neuroblastoma (NB) is the most common extra-cranial solid tumor in childhood. Very few genes in recurrent deletion regions have been identified as tumor suppressors for NB, and interactions among proteins encoded by genes in these regions have been overlooked. This study aims to identify possible tumor suppressor genes located within regions commonly deleted in NB tumors and to show possible interaction network of proteins encoded by genes in these regions by bioinformatics analysis.
View Article and Find Full Text PDFDatabase (Oxford)
February 2012
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
The reversible phosphorylation of serine, threonine and tyrosine hydroxyl groups is an especially prominent form of post-translational modification (PTM) of proteins. It plays critical roles in the regulation of diverse processes, and mutations that directly or indirectly affect these phosphorylation events have been associated with many cancers and other pathologies. Here, we describe the development of a new BioMart tool that gathers data from three different biological resources to provide the user with an integrated view of phosphorylation events associated with a human protein of interest, the complexes of which the protein (modified or not) is a part, the reactions in which the protein and its complexes participate and the somatic mutations that might be expected to perturb those functions.
View Article and Find Full Text PDFDatabase (Oxford)
February 2012
Ontario Institute for Cancer Research, Toronto, ON, M5G0A3, Canada.
Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Reactome BioMart provides biologists and bioinformaticians with a single web interface for performing simple or elaborate queries of the Reactome database, aggregating data from different sources and providing an opportunity to integrate experimental and computational results with information relating to biological pathways.
View Article and Find Full Text PDFDatabase (Oxford)
October 2011
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
We describe the Pancreatic Expression Database (PED), the first cancer database originally designed based on the BioMart infrastructure. The PED portal brings together multidimensional pancreatic cancer data from the literature including genomic, proteomic, miRNA and gene expression profiles. Based on the BioMart 0.
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