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I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study

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Protein & Cell

Higher Education Press

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      Most cited references 13

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      Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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        An Integrated Encyclopedia of DNA Elements in the Human Genome

        Summary The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall the project provides new insights into the organization and regulation of our genes and genome, and an expansive resource of functional annotations for biomedical research.
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          Data, information, knowledge and principle: back to metabolism in KEGG

          In the hierarchy of data, information and knowledge, computational methods play a major role in the initial processing of data to extract information, but they alone become less effective to compile knowledge from information. The Kyoto Encyclopedia of Genes and Genomes (KEGG) resource (http://www.kegg.jp/ or http://www.genome.jp/kegg/) has been developed as a reference knowledge base to assist this latter process. In particular, the KEGG pathway maps are widely used for biological interpretation of genome sequences and other high-throughput data. The link from genomes to pathways is made through the KEGG Orthology system, a collection of manually defined ortholog groups identified by K numbers. To better automate this interpretation process the KEGG modules defined by Boolean expressions of K numbers have been expanded and improved. Once genes in a genome are annotated with K numbers, the KEGG modules can be computationally evaluated revealing metabolic capacities and other phenotypic features. The reaction modules, which represent chemical units of reactions, have been used to analyze design principles of metabolic networks and also to improve the definition of K numbers and associated annotations. For translational bioinformatics, the KEGG MEDICUS resource has been developed by integrating drug labels (package inserts) used in society.
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            Author and article information

            Affiliations
            Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101 China
            Contributors
            wangjing@psych.ac.cn
            Journal
            Protein Cell
            Protein Cell
            Protein & Cell
            Higher Education Press (Heidelberg )
            1674-800X
            1674-8018
            20 November 2014
            20 November 2014
            March 2015
            : 6
            : 3
            : 221-224
            25407412
            4348241
            114
            10.1007/s13238-014-0114-4
            © The Author(s) 2014

            Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

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            © HEP and Springer 2015

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