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rdf:type |
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lifeskim:mentions |
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pubmed:dateCreated |
2010-7-14
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pubmed:abstractText |
Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology and progression, while revealing potentially new biomarkers. We have examined a recently developed high-throughput technology for measuring genome-wide methylation patterns called mTACL. Here, we propose a computational pipeline for integrating gene expression and CpG island methylation profiles to identify epigenetically regulated genes for a panel of 45 breast cancer cell lines, which is widely used in the Integrative Cancer Biology Program (ICBP). The pipeline (i) reduces the dimensionality of the methylation data, (ii) associates the reduced methylation data with gene expression data, and (iii) ranks methylation-expression associations according to their epigenetic regulation. Dimensionality reduction is performed in two steps: (i) methylation sites are grouped across the genome to identify regions of interest, and (ii) methylation profiles are clustered within each region. Associations between the clustered methylation and the gene expression data sets generate candidate matches within a fixed neighborhood around each gene. Finally, the methylation-expression associations are ranked through a logistic regression, and their significance is quantified through permutation analysis.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-10799744,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-10922411,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-12084816,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-12154405,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-12702564,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-15231656,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-15911243,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-16506101,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-16585505,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-17157791,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-17473312,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-17899364,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-18024971,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-18340528,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-18518979,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-18664619,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-19153192,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-9138084,
http://linkedlifedata.com/resource/pubmed/commentcorrection/20525369-9481475
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
http://linkedlifedata.com/resource/pubmed/chemical/Antigens, Neoplasm,
http://linkedlifedata.com/resource/pubmed/chemical/Collagen Type I,
http://linkedlifedata.com/resource/pubmed/chemical/DNA Topoisomerases, Type II,
http://linkedlifedata.com/resource/pubmed/chemical/DNA topoisomerase II alpha,
http://linkedlifedata.com/resource/pubmed/chemical/DNA-Binding Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Proto-Oncogene Proteins c-vav,
http://linkedlifedata.com/resource/pubmed/chemical/TFF1 protein, human,
http://linkedlifedata.com/resource/pubmed/chemical/Tumor Suppressor Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/VAV3 protein, human,
http://linkedlifedata.com/resource/pubmed/chemical/collagen type I, alpha 1 chain
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pubmed:status |
MEDLINE
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pubmed:issn |
1471-2105
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pubmed:author |
pubmed-author:CarltonVictoria E HVE,
pubmed-author:DurinckSteffenS,
pubmed-author:FahamMalekM,
pubmed-author:FlaucherDianeD,
pubmed-author:GrayJoe WJW,
pubmed-author:LossLeandro ALA,
pubmed-author:MoorheadMartinM,
pubmed-author:NautiyalShivaniS,
pubmed-author:ParvinBahramB,
pubmed-author:RazmaraMM,
pubmed-author:SadanandamAngurajA,
pubmed-author:SpellmanPaulP
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pubmed:issnType |
Electronic
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pubmed:volume |
11
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
305
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pubmed:dateRevised |
2010-11-18
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pubmed:meshHeading |
pubmed-meshheading:20525369-Antigens, Neoplasm,
pubmed-meshheading:20525369-Breast Neoplasms,
pubmed-meshheading:20525369-Cell Line, Tumor,
pubmed-meshheading:20525369-Collagen Type I,
pubmed-meshheading:20525369-CpG Islands,
pubmed-meshheading:20525369-DNA Methylation,
pubmed-meshheading:20525369-DNA Topoisomerases, Type II,
pubmed-meshheading:20525369-DNA-Binding Proteins,
pubmed-meshheading:20525369-Epigenesis, Genetic,
pubmed-meshheading:20525369-Gene Expression Profiling,
pubmed-meshheading:20525369-Gene Expression Regulation, Neoplastic,
pubmed-meshheading:20525369-Genes, Tumor Suppressor,
pubmed-meshheading:20525369-Genome-Wide Association Study,
pubmed-meshheading:20525369-Humans,
pubmed-meshheading:20525369-Oligonucleotide Array Sequence Analysis,
pubmed-meshheading:20525369-Promoter Regions, Genetic,
pubmed-meshheading:20525369-Proto-Oncogene Proteins c-vav,
pubmed-meshheading:20525369-Tumor Suppressor Proteins
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pubmed:year |
2010
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pubmed:articleTitle |
Prediction of epigenetically regulated genes in breast cancer cell lines.
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pubmed:affiliation |
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. laloss@lbl.gov
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.,
Research Support, N.I.H., Extramural
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