Pathway Resources
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KEGG: Kyoto Encyclopedia of Genes and Genomes
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
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WikiPathways
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons.
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Pathway Interaction Database
The National Cancer Institute (NCI) in collaboration with Nature Publishing Group has established the Pathway Interaction Database (PID) in order to provide a highly structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signalling pathways.
PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells.
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Invitrogen LINNEA Pathway
LINNEA™ Pathways is a collection of 248 detailed, interactive maps of interconnected biological signalling and metabolic pathways. These maps have been created for Invitrogen by GeneGo, a company that develops analytical tools, data content, and algorithms for understanding complex biological system pathways.
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MACPAK: Simulatable Macrophage Pathway Knowledgebase
MACPAK is a knowledge-base dedicated to compile the information of macrophage signal transduction pathway and their dynamics. Macrophages are distributed in peripheral tissues where they eliminate invading exogenous substances and are therefore responsible for innate immunity. They trigger acquired immunity by capturing exogenous antigens engulfing them in cellular lysosomes. Significant progress has been made recently in understanding the biochemical mechanisms by which lopopolysaccharide (LPS) activates immune cells, particularly macrophages by analyzing quantitative microarray time course data.
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Nature: Lipid Maps
LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.
Innate Immunity Resources
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The Macrophage Community Website
Macrophages.com is an online resource for those interested in macrophages and their role as major effector cells in innate and adaptive immunity. The website is designed to act as a centralised resource for the worldwide community of scientists interested in different aspects of macrophage biology. Included are:
- Collections of macrophage images in different tissues
- Expression datasets and transcriptional analyses
- Analysis of protein expression in macrophages
- A gene-centered information portal for macrophage-expressed genes
- Macrophage pathway resources
- Curated key publications and reviews on aspects of macrophage biology
- Useful online resources
- News and events
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Innate Immunity Interactions and Pathways Database
InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.
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The Immunome Database
The immune system is a complex machinery, which is based on the highly coordinated expression of a wide array of genes and proteins. Internet resource called Immunome was constructed for the characterisation of the human immune system. Immunome contains information about immunity related proteins, their domain structure and the related ontology terms. Information can be found also about the localization of the coding genesand their comparison with the existing mouse orthologs. In addition links to the ImmTree database are also included for phylogenetic trees for orthologs from 104 species.
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The Immunological Genome Project
The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression microarray database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the genetic regulatory network in immune cells. All data generated as part of ImmGen are made freely and publicly available.
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Immune Modeling Community
The Immune Modeling Community Web Portal. This website features news and resources relevant to investigators interested in immune response modeling for infectious disease research. The purpose of the website is to facilitate collaboration and exchange information (including data, models, publications, events, funding opportunities) among researchers interested in using, developing and validating mathematical models of the immune response to infectious diseases.
Interaction Databases
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Innate Immunity Interactions and Pathways Database
InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.
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MACPAK: Simulatable Macrophage Pathway Knowledgebase
MACPAK is a knowledge-base dedicated to compile the information of macrophage signal transduction pathway and their dynamics. Macrophages are distributed in peripheral tissues where they eliminate invading exogenous substances and are therefore responsible for innate immunity. They trigger acquired immunity by capturing exogenous antigens engulfing them in cellular lysosomes. Significant progress has been made recently in understanding the biochemical mechanisms by which lopopolysaccharide (LPS) activates immune cells, particularly macrophages by analyzing quantitative microarray time course data.
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Human Protein Reference Database
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.
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PATRIC – Host-Pathogen Interaction Database
PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. PATRIC sharpens and hones the scope of available bacterial phylogenomic data from numerous sources specifically for the bacterial research community, in order to save biologists time and effort when conducting comparative analyses. The freely available PATRIC platform provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses in a one-stop shop. PATRIC is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division.
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Database of Interacting Proteins (DIP)
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
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GeneMANIA
GeneMANIA helps you predict the function of your favourite genes and gene sets. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input.
Additional Resources
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Human Monocytes in Health and Disease
Monocytes develop from myelo-monocytic stem cells in the bone marrow. They then go into blood, where they circulate for a few days in order to then migrate into tissues. In the tissue they further mature into macrophages. Tissue macrophages are extremely heterogenous dependent on the type of tissue (microglial cells in the brain, alveolar macrophages in the lung, osteoclasts in bone) and on the process (giant cells in granuloma, tumor associated macrophages in malignancy).
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The European Macrophage and Dendritic Cell Society (EMDS)
The European Macrophage and Dendritic Cell Society (EMDS) has emerged from the activities of the former European Macrophage Study Group (EMSG), a loose association of scientists interested in basic and clinical aspects of monocytes, macrophages, dendritic cells and other myleoid cells in man and experimental animal models.
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Macrophage Comparative Expression Gateway
MacGate is a publicly available resource focused on divergent gene regulation in human and mouse macrophages. The website displays expression data generated from a custom microarray, which were specifically collected and analysed to investigate divergent gene regulation in response to lipopolysaccharide (LPS), a component of Gram-negative bacterial cell walls that stimulates inflammatory responses via Toll-like receptor 4.
Other
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OMICtools
OMICtools is a free metadatabase for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR). OMICtools is expected to serve as a useful didactic resource not only for bioinformaticians, but also for experimental researchers and clinicians.
©
The Roslin Institute 2016