{"data":{"id":"10.6084/m9.figshare.1568111","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1568111","prefix":"10.6084","suffix":"m9.figshare.1568111","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Md Almamun","affiliation":[],"nameIdentifiers":[]},{"name":"Levinson, Benjamin T","nameType":"Personal","givenName":"Benjamin T","familyName":"Levinson","affiliation":[],"nameIdentifiers":[]},{"name":"Swaay, Annette C Van","nameType":"Personal","givenName":"Annette C Van","familyName":"Swaay","affiliation":[],"nameIdentifiers":[]},{"name":"Johnson, Nathan T","nameType":"Personal","givenName":"Nathan T","familyName":"Johnson","affiliation":[],"nameIdentifiers":[]},{"name":"McKay, Stephanie D","nameType":"Personal","givenName":"Stephanie D","familyName":"McKay","affiliation":[],"nameIdentifiers":[]},{"name":"Arthur, Gerald L","nameType":"Personal","givenName":"Gerald L","familyName":"Arthur","affiliation":[],"nameIdentifiers":[]},{"name":"J Wade Davis","affiliation":[],"nameIdentifiers":[]},{"name":"Taylor, Kristen H","nameType":"Personal","givenName":"Kristen H","familyName":"Taylor","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Biochemistry"},{"subject":"Medicine"},{"subject":"Cell Biology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"59999 Environmental Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Earth and related environmental sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Earth and related environmental sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"Developmental Biology"},{"subject":"Cancer"},{"subject":"Hematology"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2015-10-08","dateType":"Created"},{"date":"2016-03-11","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15592294.2015.1078050","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["3852488 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as \u003ci\u003eSYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1\u003c/i\u003e, and \u003ci\u003eMELK\u003c/i\u003e, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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