Linked Life Data

18490134

Source:http://linkedlifedata.com/resource/pubmed/id/18490134

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
2008-6-9
pubmed:abstractText
Microarray analysis of formalin-fixed and paraffin-embedded (FFPE) tissue seems to be of importance for the detection of molecular marker sets in prostate cancer (PC). The compromised RNA integrity of FFPE tissue results in a high degree of variability at the probe level of microarray data as shown by degradation plot. We tested methods that reduce the variability by including all probes within 300 nucleotides, within 600 nucleotides, or up to a calculated breakpoint with reference to the 3'-end. Accepted PC pathways such as the Wnt signaling pathway could be observed to be significantly regulated within FFPE microarray datasets. The best representation of PC gene expression, as well as better comparability to meta-analysis and fresh-frozen microarray data, could be obtained with a 600-nucleotide cutoff. Beyond the specific impact for PC microarray data analysis we propose a cutoff of 600 nucleotides for samples for which the integrity of the RNA cannot be guaranteed.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
1089-8646
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
91
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
522-9
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
A cut-off based approach for gene expression analysis of formalin-fixed and paraffin-embedded tissue samples.
pubmed:affiliation
Department of Cellular and Molecular Pathology, German Cancer Research Center, D-69120 Heidelberg, Germany.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't