{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:29:50Z","timestamp":1791332990702,"version":"4.3.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T00:00:00Z","timestamp":1475625600000},"content-version":"vor","delay-in-days":1475,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"DOI":"10.1093\/nar\/gks866","type":"journal-article","created":{"date-parts":[[2012,9,22]],"date-time":"2012-09-22T20:44:50Z","timestamp":1348346690000},"page":"e19-e19","source":"Crossref","is-referenced-by-count":108,"title":["Along signal paths: an empirical gene set approach exploiting pathway topology"],"prefix":"10.1093","volume":"41","author":[{"given":"Paolo","family":"Martini","sequence":"first","affiliation":[{"name":"CRIBI Biotechnology Center, 2Department of Biology, University of Padova, via U. Bassi 58\/B, 35121 Padova, Italy, 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK and 4Department of Statistical Science, University of Padova, via C. Battisti 241, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Sales","sequence":"additional","affiliation":[{"name":"CRIBI Biotechnology Center, 2Department of Biology, University of Padova, via U. Bassi 58\/B, 35121 Padova, Italy, 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK and 4Department of Statistical Science, University of Padova, via C. Battisti 241, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Sofia","family":"Massa","sequence":"additional","affiliation":[{"name":"CRIBI Biotechnology Center, 2Department of Biology, University of Padova, via U. Bassi 58\/B, 35121 Padova, Italy, 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK and 4Department of Statistical Science, University of Padova, via C. Battisti 241, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica","family":"Chiogna","sequence":"additional","affiliation":[{"name":"CRIBI Biotechnology Center, 2Department of Biology, University of Padova, via U. Bassi 58\/B, 35121 Padova, Italy, 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK and 4Department of Statistical Science, University of Padova, via C. Battisti 241, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[{"name":"CRIBI Biotechnology Center, 2Department of Biology, University of Padova, via U. Bassi 58\/B, 35121 Padova, Italy, 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK and 4Department of Statistical Science, University of Padova, via C. Battisti 241, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,9,21]]},"reference":[{"key":"key\n\t\t\t\t20180801055104_gks866-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"Smyth","year":"2004","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"key\n\t\t\t\t20180801055104_gks866-B2","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180801055104_gks866-B3","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: aknowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180801055104_gks866-B4","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1101\/gr.6202607","article-title":"A systems biology approach for pathway level analysis","volume":"17","author":"Draghici","year":"2007","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B5","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","article-title":"Analyzing gene expression data in terms of gene sets: methodological issues","volume":"23","author":"Goeman","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B6","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1093\/bioinformatics\/btr269","article-title":"Pathway analysis of high-throughput biological data within a Bayesian network framework","volume":"27","author":"Isci","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B7","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1089\/cmb.2007.0041","article-title":"The chronic fatigue syndrome: a comparative pathway analysis","volume":"14","author":"Emmert-Streib","year":"2007","journal-title":"J. Comput. Biol."},{"key":"key\n\t\t\t\t20180801055104_gks866-B8","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1471-2105-10-47","article-title":"A general modular framework for gene set enrichment analysis","volume":"10","author":"Ackermann","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B9","doi-asserted-by":"crossref","first-page":"13544","DOI":"10.1073\/pnas.0506577102","article-title":"Discovering statistically significant pathways in expression profiling studies","volume":"102","author":"Tian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180801055104_gks866-B10","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180801055104_gks866-B11","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","article-title":"A novel signaling pathway impact analysis","volume":"25","author":"Tarca","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B12","first-page":"561","article-title":"Gains in power from structured two-sample tests of means on graphs","volume":"6","author":"Laurent","year":"2012","journal-title":"Ann. Appl. Stat."},{"key":"key\n\t\t\t\t20180801055104_gks866-B13","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/1752-0509-4-121","article-title":"Gene set analysis exploiting the topology of a pathway","volume":"4","author":"Massa","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"key\n\t\t\t\t20180801055104_gks866-B14","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2105-13-20","article-title":"graphite - a Bioconductor package to convert pathway topology to gene network","volume":"13","author":"Sales","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B15","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"27","author":"Ogata","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B16","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the pathway interaction database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B17","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1093\/nar\/gkn863","article-title":"Reactome knowledgebase of human biological pathways and processes","volume":"37","author":"Matthews","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B18","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/1471-2105-13-167","article-title":"Network-enabled gene expression analysis","volume":"13","author":"Edwards","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B19","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198522195.001.0001","volume-title":"Graphical Models","author":"Lauritzen","year":"1996"},{"key":"key\n\t\t\t\t20180801055104_gks866-B20","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1175","article-title":"A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics","volume":"4","author":"Schafer","year":"2005","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"key\n\t\t\t\t20180801055104_gks866-B21","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1252","article-title":"Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach","volume":"6","author":"Opgen-Rhein","year":"2007","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"key\n\t\t\t\t20180801055104_gks866-B22","first-page":"2621","article-title":"A robust procedure for Gaussian graphical model search from microarray data with p larger than n","volume":"7","author":"Castelo","year":"2006","journal-title":"J. Mach. Learn. Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B23","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1093\/biostatistics\/kxm045","article-title":"Sparse inverse covariance estimation with the graphical lasso","volume":"9","author":"Friedman","year":"2008","journal-title":"Biostatistics"},{"key":"key\n\t\t\t\t20180801055104_gks866-B24","doi-asserted-by":"crossref","first-page":"7209","DOI":"10.1158\/1078-0432.CCR-04-2165","article-title":"Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation","volume":"11","author":"Chiaretti","year":"2005","journal-title":"Clin. Cancer Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B25","doi-asserted-by":"crossref","first-page":"e175","DOI":"10.1093\/nar\/gni179","article-title":"Evolving gene\/transcript definitions significantly alter the interpretation of GeneChip data","volume":"33","author":"Dai","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180801055104_gks866-B26","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1038\/nrc1567","article-title":"Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia","volume":"5","author":"Ren","year":"2005","journal-title":"Nat. Rev. Cancer"},{"key":"key\n\t\t\t\t20180801055104_gks866-B27","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1016\/j.bbrc.2005.03.152","article-title":"C-Abl as a modulator of p53","volume":"331","author":"Levav-Cohen","year":"2005","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"key\n\t\t\t\t20180801055104_gks866-B28","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1093\/brain\/awl023","article-title":"Nuclear envelope dystrophies showa transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration","volume":"129","author":"Bakay","year":"2006","journal-title":"Brain"},{"key":"key\n\t\t\t\t20180801055104_gks866-B29","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/0092-8674(95)90368-2","article-title":"Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A","volume":"81","author":"Richard","year":"1995","journal-title":"Cell"},{"key":"key\n\t\t\t\t20180801055104_gks866-B30","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1093\/hmg\/ddi217","article-title":"Calpain 3 participates in sarcomere remodeling by acting upstream of the ubiquitin\u2013proteasome pathway","volume":"14","author":"Kramerova","year":"2005","journal-title":"Hum. Mol. Genet."},{"key":"key\n\t\t\t\t20180801055104_gks866-B31","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature01573","article-title":"Defective membrane repair in dysferlin-deficient muscular dystrophy","volume":"423","author":"Bansal","year":"2003","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180801055104_gks866-B32","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1093\/hmg\/ddn081","article-title":"Calpain 3 is a modulator of the dysferlin protein complex in skeletal muscle","volume":"17","author":"Huang","year":"2008","journal-title":"Hum. Mol. Genet."},{"key":"key\n\t\t\t\t20180801055104_gks866-B33","doi-asserted-by":"crossref","first-page":"4322","DOI":"10.1111\/j.1742-4658.2010.07820.x","article-title":"Anewpathway encompassing calpain 3 and its newly identified substrate cardiac ankyrin repeat protein is involved in the regulation of the nuclear factor-kB pathway in skeletal muscle","volume":"277","author":"Laure","year":"2010","journal-title":"FEBS J."},{"key":"key\n\t\t\t\t20180801055104_gks866-B34","first-page":"3966","article-title":"MicroRNA expression profiling in patients with lamin A\/C-associated muscular dystrophy","volume":"25","author":"Sylvius","year":"2011","journal-title":"FASEB J., Off. Publ. Fed. Am. Soc. Exp. Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/1\/e19\/25348953\/gks866.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T14:26:13Z","timestamp":1714400773000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/41\/1\/e19\/1170622"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,21]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2012,9,21]]},"published-print":{"date-parts":[[2013,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gks866","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1,7]]},"published":{"date-parts":[[2012,9,21]]}}}