Marc Gillespie

St. John's University

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Peter D’Eustachio

New York University

Guanming Wu

Oregon Health & Science University

Lisa Matthews

Columbia University Irving Medical Center

Bijay Jassal

Ontario Institute for Cancer Research

Lincoln Stein

Ontario Institute for Cancer Research

Henning Hermjakob

European Bioinformatics Institute

Robin Haw

Ontario Institute for Cancer Research

Ewan Birney

European Bioinformatics Institute

M Orlic-Milacic

Ontario Institute for Cancer Research

Veronica Shamovsky

New York University

Cooperative Institutions

European Bioinformatics Institute

National Institute of Advanced Industrial Science and Technology

Dankook University

Wellcome Trust

Stanford University

Cold Spring Harbor Laboratory

Ontario Institute for Cancer Research

National Center for Biotechnology Information

Northwestern University

University College London

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Biomarker discovery and compound evaluation using two-hybrid proteomic systems

Expert Opinion on Drug Discovery (2006)

Marc Gillespie

Many proteomic technologies require a heavy investment in expertise and technology, which place these approaches beyond many labs and small companies. However, proteomic approaches are ideal for pilot experiments, identifying relevant biomarkers and protein pathways for development or analysis of therapeutic compounds. The two-hybrid proteomic systems are available and affordable to most researchers, requiring little more than standard microbiological equipment. The screens rapidly generate data, identifying protein interactions that can be used to construct small local protein networks. Using data from large-scale projects, these small local protein networks can be used to identify the larger cellular pathways that are being affected by therapeutic compounds in the screen. The foundation for the two-hybrid proteomic systems are commercially available, as are high quality cDNA libraries. The straightforwardness of the two-hybrid proteomic system allows smaller groups to focus their resources on critical cellular pathways and molecular targets by taking advantage of a trusted molecular assay and an ever growing set of postgenomic era databases.

Biomarker Discovery

10.1517/17460441.1.5.389

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Guidelines for the functional annotation of microRNAs using the Gene Ontology

RNA (2016)

Rachael P. Huntley Д. С. Ситников M Orlic-Milacic Rama Balakrishnan Peter D’Eustachio

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual).

Gene Annotation

10.1261/rna.055301.115

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Citations (42)

Clathrin derived vesicle budding

Reactome - a curated knowledgebase of biological pathways (2009)

Marc Gillespie

Budding

10.3180/react_19187.1

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Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

Nature Biotechnology (2012)

Emek Demir Michael P. Cary Suzanne Paley Ken Fukuda Christian Lemer

Nat

10.1038/nbt0412-365c

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The reactome pathway knowledgebase

Nucleic Acids Research (2019)

Bijay Jassal Lisa Matthews Guilherme Viteri Chuqiao Gong Pascual Lorente

Abstract The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.

Upload

10.1093/nar/gkz1031

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Citations (2,035)

Reactome - a knowledgebase of human biological pathways

Nature Precedings (2009)

Bijay Jassal Esther Schmidt Guanming Wu Imre Västrik David Croft

Abstract Reactome ("http://www.reactome.org":http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms. Reactome instances are cross-referenced to corresponding ones in databases including EntrezGene, OMIM, Ensembl, UniProt, the UCSC Genome Browser, KEGG, ChEBI, and Gene Ontology.

UniProt

Ensembl

KEGG

10.1038/npre.2009.3200.1

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Golgi to ER Retrograde Transport

Reactome - a curated knowledgebase of biological pathways (2007)

Marc Gillespie

Axoplasmic transport

10.3180/react_11208.1

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Innate Immunity Signaling

Reactome - a curated knowledgebase of biological pathways (2008)

Bernard de Bono Marc Gillespie Feifei Luo NJ Gay

10.3180/react_6802.2

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Citations (1)

Fertilization

Reactome - a curated knowledgebase of biological pathways (2013)

Marc Gillespie

10.3180/react_163914.1

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Small‐Interfering RNA‐Mediated Identification and Regulation of the Ternary SNARE Complex Mediating RBL‐2H3 Mast Cell Degranulation

Scandinavian Journal of Immunology (2010)

Joseph R. Woska Marc Gillespie

Abstract Dysregulation of mast cell function contributes to allergic and autoimmune disease that affects more than 70 million persons in the United States alone. Identifying novel mast cell targets that mediate disease or disease progression is required for the development of innovative therapeutics for the treatment of allergy/asthma and autoimmune disease. RNA interference technologies offer hope both as basic research tools for target identification and as potential, novel, specific therapeutics. Soluble N ‐ethylmaleimide‐sensitive factor attachment protein receptors (SNAREs) are a family of evolutionarily conserved proteins that have been postulated to mediate the transport and fusion of inflammatory mediator‐laden vesicles to the membrane in mast cells leading to their subsequent exocytosis. The functional role(s) of specific SNARE family member complexes in mast cell degranulation has not been fully elucidated. Here, we characterize the functional importance of SNARE complexes in FcεRI receptor‐mediated degranulation of RBL‐2H3 cells utilizing RNA interference. We demonstrate that ternary SNARE complexes of synaptosomal‐associated protein‐23, Syntaxin 4 and vesicle‐associated membrane protein‐7 (VAMP‐7) or VAMP‐8 are directly involved in mast cell degranulation. Additionally, we evaluate the siRNAs directed against these molecules as potential therapeutic agents for disease intervention. These studies have identified specific SNARE proteins and complexes that serve as novel targets for the development of siRNA therapies to treat allergic and autoimmune disease.

10.1111/j.1365-3083.2010.02471.x

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Citations (33)