http://precedings.nature.com/tags/pathways Recently posted documents tagged with 'pathways' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3447/version/1 Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs after PTZ discontinuation exhibited normal climbing speed on 7th day, i.e., 14th day from the beginning of PTZ treatment. Time-series of microarray expression profiles of fly heads comparing control PTZ- and AED-untreated, and AED-untreated post PTZ withdrawal groups showed differentially expressed genes throughout. These genes enriched gene ontology (GO) molecular functions including transcription regulator and GTPase regulator activities. Interestingly, expression profiles of fly heads comparing control PTZ- and AED-untreated, and AED-treated post PTZ withdrawal groups showed neutralization of transcription regulator and GTPase regulator activities by the AEDs. Further transcriptomic analysis based on overinteraction in protein interactome and enrichment of miRNA targets implicated axon guidance and neuronal remodeling related perturbations in the fly model. Differential expression of genes belonging to transcription regulator and GTPase regulator activities have previously been reported in post-epileptogenesis in established rodent models. Also, axon guidance and neuronal remodeling related alterations have been implicated in epilepsy. The Drosophila model thus provides a unique opportunity to dissect long-term plasticity relevant in epileptogenesis at cellular and molecular levels. Besides, the model also offers an excellent system to efficiently screen agents with potential therapeutic activity. http://precedings.nature.com/documents/3447/version/1 Tue, 21 Jul 2009 16:40:03 UTC A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis hdl:10101/npre.2009.3447.1 2009-07-21 Abhay Sharma Nature Precedings 2009-07-21T16:40:03Z Manuscript Genetics & Genomics Neuroscience Pharmacology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3200.1 Reactome (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. http://dx.doi.org/10.1038/npre.2009.3200.1 Sun, 03 May 2009 15:44:21 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2009.3200.1 2009-05-07 Bijay Jassal Nature Precedings 2009-05-03T15:44:21Z Poster Chemistry Genetics & Genomics Immunology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3115.1 Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal mechanism, webservice and pathway extension through automated suggestions. http://dx.doi.org/10.1038/npre.2009.3115.1 Tue, 21 Apr 2009 17:07:45 UTC Community curation on WikiPathways: How we assist knowledge collection doi:10.1038/npre.2009.3115.1 2009-04-21 Chris Evelo Nature Precedings 2009-04-21T17:07:45Z Presentation Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2041/version/1 A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes. Surprisingly, the small repertoire of HIV proteins also interferes loosely with many signaling and regulation pathways, suggesting that a widespread involvement in such pathways secures the control of the host cell. Such insights offer novel perspectives to investigate the progression of HIV infection and potentially can contribute to our abilities to fight this virus. http://precedings.nature.com/documents/2041/version/1 Wed, 09 Jul 2008 17:18:11 UTC Viral organization of human proteins hdl:10101/npre.2008.2041.1 2008-07-09 Stefan Wuchty Nature Precedings 2008-07-09T17:18:11Z Manuscript Microbiology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1311.1 The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely availablecollection of curated and peer-reviewed signaling pathways composed of humanbiomolecular interactions and cellular processes. Created in a collaboration between theU.S. National Cancer Institute and Nature Publishing Group, the database is a researchtool for cell biologists, biochemists, computational biologists and bioinformaticians.The PID offers a range of tools to facilitate pathway exploration. Users can browse thepre-defi ned set of pathways and also create interaction network maps centered ona single molecule of interest or an extensive list of molecules. In addition, users candownload complete data sets in extensible markup language (XML) and BiologicalPathway Exchange (BioPAX) Level 2 formats. The database is updated every month andsupplemented by a concise editorial section that provides synopses of recent noteworthypapers in cell signaling and specially commissioned articles on the practical uses ofother relevant online tools. Users can sign up for free email alerts or RSS feeds to receivedatabase updates. http://dx.doi.org/10.1038/npre.2007.1311.1 Mon, 12 Nov 2007 16:51:55 UTC The NCI-Nature Pathway Interaction Database: A cell signaling resource. doi:10.1038/npre.2007.1311.1 2007-11-12 Kira Anthony Nature Precedings 2007-11-12T16:51:55Z Poster Cancer Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/