Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of human normal pre-frontal cortex, liver, and colon tissues and colon tumors

ABSTRACT: DNA methylation, at CpG islands and promoters, is often inversely correlated with gene expression. We used expression microarrays to determine the relationship between DNA methylation and gene expression in 5 normal prefrontal cortex samples and 5 normal liver samples from the same individuals as well as between 4 colon tumor and matched normal colon mucosa (from the same individuals). Experiment Overall Design: We isolated RNA from pre-frontal cortex and liver tissue from 5 individuals for which we have genome-wide DNA methylation data and hybridized to Affymetrix gene expression microarrays. Similarly, we isolated RNA from 4 tumor and matched normal colon samples that we have genome-wide DNA methylation data..

This experiment was reloaded in November 2010 after additional curation.

ORGANISM(S): Homo sapiens

SUBMITTER: rafael irizarry 

PROVIDER: E-GEOD-13471 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.

Irizarry Rafael A RA   Ladd-Acosta Christine C   Wen Bo B   Wu Zhijin Z   Montano Carolina C   Onyango Patrick P   Cui Hengmi H   Gabo Kevin K   Rongione Michael M   Webster Maree M   Ji Hong H   Potash James J   Sabunciyan Sarven S   Feinberg Andrew P AP  

Nature genetics 20090118 2

For the past 25 years, it has been known that alterations in DNA methylation (DNAm) occur in cancer, including hypomethylation of oncogenes and hypermethylation of tumor suppressor genes. However, most studies of cancer methylation have assumed that functionally important DNAm will occur in promoters, and that most DNAm changes in cancer occur in CpG islands. Here we show that most methylation alterations in colon cancer occur not in promoters, and also not in CpG islands, but in sequences up to  ...[more]

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