{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670320190292864.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1093/bioinformatics/btt684"}},{"identifier":{"@type":"URI","@value":"https://academic.oup.com/bioinformatics/article-pdf/30/3/428/48914550/bioinformatics_30_3_428.pdf"}}],"dc:title":[{"@value":"ChAMP: 450k Chip Analysis Methylation Pipeline"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title>\n               <jats:p>The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and processing of these data have been published recently. Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.</jats:p>\n               <jats:p>Availability and implementation: ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org</jats:p>\n               <jats:p>Contact:  tiffany.morris@ucl.ac.uk</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383670320190292865","@type":"Researcher","foaf:name":[{"@value":"Tiffany J. Morris"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292866","@type":"Researcher","foaf:name":[{"@value":"Lee M. Butcher"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292736","@type":"Researcher","foaf:name":[{"@value":"Andrew Feber"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292869","@type":"Researcher","foaf:name":[{"@value":"Andrew E. Teschendorff"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"},{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292868","@type":"Researcher","foaf:name":[{"@value":"Ankur R. Chakravarthy"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292864","@type":"Researcher","foaf:name":[{"@value":"Tomasz K. Wojdacz"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670320190292867","@type":"Researcher","foaf:name":[{"@value":"Stephan Beck"}],"jpcoar:affiliationName":[{"@value":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"13674811"},{"@type":"PISSN","@value":"13674803"}],"prism:publicationName":[{"@value":"Bioinformatics"}],"dc:publisher":[{"@value":"Oxford University Press (OUP)"}],"prism:publicationDate":"2013-12-12","prism:volume":"30","prism:number":"3","prism:startingPage":"428","prism:endingPage":"430"},"reviewed":"false","url":[{"@id":"https://academic.oup.com/bioinformatics/article-pdf/30/3/428/48914550/bioinformatics_30_3_428.pdf"}],"createdAt":"2013-12-14","modifiedAt":"2023-01-27","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050564288162532864","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Integrative genomic analysis of adult mixed phenotype acute leukemia delineates lineage associated molecular subtypes"},{"@value":"Futreal: Integrative Genomic Analysis of Adult Mixed Phenotype Acute Leukemia Delineates Lineage Associated Molecular Subtypes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360004233963717120","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Neuron-specific methylome analysis reveals epigenetic regulation and tau-related dysfunction of BRCA1 in Alzheimer’s disease"}]},{"@id":"https://cir.nii.ac.jp/crid/1360009142766282880","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genome-wide methylation analysis in Silver–Russell syndrome, Temple syndrome, and Prader–Willi syndrome"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013168812301056","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Epigenetic Changes in Neonates Born to Mothers With Gestational Diabetes Mellitus May Be Associated With Neonatal Hypoglycaemia"}]},{"@id":"https://cir.nii.ac.jp/crid/1360017279850915584","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Novel compound heterozygous mutations in <i>UHRF1</i> are associated with atypical immunodeficiency, centromeric instability and facial anomalies syndrome with distinctive genome-wide DNA hypomethylation"}]},{"@id":"https://cir.nii.ac.jp/crid/1360283693139788800","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of the genomic region under epigenetic regulation during non‐alcoholic fatty liver disease progression"}]},{"@id":"https://cir.nii.ac.jp/crid/1360283693944969984","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285708465240320","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of differentially methylated region (DMR) networks associated with progression of nonalcoholic fatty liver disease"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285713249909504","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Comprehensive analysis identifying aberrant DNA methylation in rectal mucosa from ulcerative colitis patients with neoplasia"}]},{"@id":"https://cir.nii.ac.jp/crid/1360287144118218880","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genome-wide analysis of DNA methylation profile identifies differentially methylated loci associated with human intervertebral disc degeneration"}]},{"@id":"https://cir.nii.ac.jp/crid/1360290617548502912","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Attempt to Predict A/T/N-Based Alzheimer’s Disease Cerebrospinal Fluid Biomarkers Using a Peripheral Blood DNA Methylation Clock"}]},{"@id":"https://cir.nii.ac.jp/crid/1360306905606056960","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"DNA methylation changes in the genome of patients with hypogonadotropic hypogonadism"}]},{"@id":"https://cir.nii.ac.jp/crid/1360306905606568832","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Site-Specific Expression of HOXA Genes in Skin and its Effect on Skin Elasticity"}]},{"@id":"https://cir.nii.ac.jp/crid/1360565169420852224","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols"}]},{"@id":"https://cir.nii.ac.jp/crid/1360572092436478848","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360572092708836480","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data"}]},{"@id":"https://cir.nii.ac.jp/crid/1360576118678706816","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements"}]},{"@id":"https://cir.nii.ac.jp/crid/1360576118695297408","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Epigenome-wide association study of narcolepsy-affected lateral hypothalamic brains, and overlapping DNA methylation profiles between narcolepsy and multiple sclerosis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360576118768044800","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"DNA methylation analysis of cord blood samples in neonates born to gestational diabetes mothers diagnosed before 24 gestational weeks"}]},{"@id":"https://cir.nii.ac.jp/crid/1360580229796087936","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing"}]},{"@id":"https://cir.nii.ac.jp/crid/1360584340532383744","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of differentially methylated regions associated with both liver fibrosis and hepatocellular carcinoma"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848656954513920","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Methylation changes and aberrant expression of FGFR3 in Lewy body disease neurons"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848660455502976","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of core gene networks and hub genes associated with progression of non‐alcoholic fatty liver disease by RNA sequencing"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848661773627392","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Exploring the unique function of imprinting control centers in the PWS/AS-responsible region: finding from array-based methylation analysis in cases with variously sized microdeletions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360853567363798912","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders"}]},{"@id":"https://cir.nii.ac.jp/crid/1360861707151367680","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"MSIMEP: Predicting microsatellite instability from microarray DNA methylation tumor profiles"}]},{"@id":"https://cir.nii.ac.jp/crid/1361412891069342080","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Gene expression and DNA methylation changes in BeWo cells dependent on tumor necrosis factor-α and insulin-like growth factor-I"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1093/bioinformatics/btt684"},{"@type":"CROSSREF","@value":"10.1073/pnas.1707151114_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.18632/oncotarget.26032_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1186/s13148-020-00949-8_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.3389/fendo.2021.690648_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1093/hmg/ddac291_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1111/hepr.12992_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1186/1471-2164-16-s12-s3_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1038/s41467-018-04924-z_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1038/s41598-018-31886-5_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1371/journal.pone.0222188_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.3233/adr-200205_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1016/j.heliyon.2024.e37648_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1016/j.jid.2025.04.005_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1371/journal.pone.0147519_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1016/j.stem.2019.05.013_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1038/s41598-021-83016-3_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1186/s13148-021-01121-6_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1093/sleep/zsz198_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1136/bmjdrc-2021-002539_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1038/s10038-022-01083-4_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1186/s12876-024-03149-3_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1111/hepr.12877_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1186/s13148-019-0633-1_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.3390/ijms22073735_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1016/j.isci.2023.106127_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1007/s13577-019-00299-5_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"},{"@type":"CROSSREF","@value":"10.1016/j.brainres.2018.06.017_references_DOI_3wxuXqQ8wXxJJ1X2pp0kBKAsObd"}]}