{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T09:57:34Z","timestamp":1786787854505,"version":"build-2736575974"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary:Pathway-level analysis is a powerful approach enabling interpretation of post-genomic data at a higher level than that of individual biomolecules. Yet, it is currently hard to integrate more than one type of omics data in such an approach. Here, we present a web tool \u2018IMPaLA\u2019 for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. It performs over-representation or enrichment analysis with user-specified lists of metabolites and genes using over 3000 pre-annotated pathways from 11 databases. As a result, pathways can be identified that may be disregulated on the transcriptional level, the metabolic level or both. Evidence of pathway disregulation is combined, allowing for the identification of additional pathways with changed activity that would not be highlighted when analysis is applied to any of the functional levels alone. The tool has been implemented both as an interactive website and as a web service to allow a programming interface.<\/jats:p><jats:p>Availability:The web interface of IMPaLA is available at http:\/\/impala.molgen.mpg.de. A web services programming interface is provided at http:\/\/impala.molgen.mpg.de\/wsdoc.<\/jats:p><jats:p>Contact: \u00a0kamburov@molgen.mpg.de; r.cavill@imperial.ac.uk; h.keun@imperial.ac.uk<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr499","type":"journal-article","created":{"date-parts":[[2011,9,6]],"date-time":"2011-09-06T00:26:54Z","timestamp":1315268814000},"page":"2917-2918","source":"Crossref","is-referenced-by-count":372,"title":["Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA"],"prefix":"10.1093","volume":"27","author":[{"given":"Atanas","family":"Kamburov","sequence":"first","affiliation":[{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Cavill","sequence":"additional","affiliation":[{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"},{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy M. D.","family":"Ebbels","sequence":"additional","affiliation":[{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"Herwig","sequence":"additional","affiliation":[{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hector C.","family":"Keun","sequence":"additional","affiliation":[{"name":"1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, 2Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands and 3Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,9,4]]},"reference":[{"key":"2023012512013670600_B1","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1634\/stemcells.2005-0113","article-title":"Primary differentiation in the human blastocyst: Comparative molecular portraits of inner cell mass and trophectoderm cells","volume":"23","author":"Adjaye","year":"2005","journal-title":"Stem Cells"},{"key":"2023012512013670600_B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012512013670600_B3","doi-asserted-by":"crossref","first-page":"e1001113","DOI":"10.1371\/journal.pcbi.1001113","article-title":"Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells","volume":"7","author":"Cavill","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"2023012512013670600_B4","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1093\/bioinformatics\/btr001","article-title":"MBRole: enrichment analysis of metabolomic data","volume":"27","author":"Chagoyen","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512013670600_B5","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2008","journal-title":"Nat. Protocols"},{"key":"2023012512013670600_B6","doi-asserted-by":"crossref","first-page":"D712","DOI":"10.1093\/nar\/gkq1156","article-title":"ConsensusPathDB: toward a more complete picture of cell biology","volume":"39","author":"Kamburov","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512013670600_B7","doi-asserted-by":"crossref","first-page":"3141","DOI":"10.1158\/1535-7163.MCT-08-0642","article-title":"A genomic approach to identify molecular pathways associated with chemotherapy resistance","volume":"7","author":"Riedel","year":"2008","journal-title":"Mol. Cancer Therap."},{"key":"2023012512013670600_B8","doi-asserted-by":"crossref","first-page":"3868","DOI":"10.1161\/CIRCULATIONAHA.105.569137","article-title":"Metabolomic identification of novel biomarkers of myocardial ischemia","volume":"112","author":"Sabatine","year":"2005","journal-title":"Circulation"},{"key":"2023012512013670600_B9","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/73439","article-title":"A gene expression database for the molecular pharmacology of cancer","volume":"24","author":"Scherf","year":"2000","journal-title":"Nat. Genet."},{"key":"2023012512013670600_B10","doi-asserted-by":"crossref","first-page":"W71","DOI":"10.1093\/nar\/gkq329","article-title":"MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data","volume":"38","author":"Xia","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2917\/48873921\/bioinformatics_27_20_2917.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2917\/48873921\/bioinformatics_27_20_2917.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,9]],"date-time":"2025-03-09T19:07:05Z","timestamp":1741547225000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/20\/2917\/202905"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,4]]},"references-count":10,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2011,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr499","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,10,15]]},"published":{"date-parts":[[2011,9,4]]}}}