Linked Life Data

15598613

Source:http://linkedlifedata.com/resource/pubmed/id/15598613

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
16
pubmed:dateCreated
2004-12-15
pubmed:abstractText
Class prediction using "omics" data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few samples and a very large number of predictor variables (e.g., genes of DNA microarray data or m/z peaks of mass spectrometry data). These characteristics manifest the importance of assessing potential random correlation and overfitting of noise for a classification model based on omics data. We present a novel classification method, decision forest (DF), for class prediction using omics data. DF combines the results of multiple heterogeneous but comparable decision tree (DT) models to produce a consensus prediction. The method is less prone to overfitting of noise and chance correlation. A DF model was developed to predict presence of prostate cancer using a proteomic data set generated from surface-enhanced laser deposition/ionization time-of-flight mass spectrometry (SELDI-TOF MS). The degree of chance correlation and prediction confidence of the model was rigorously assessed by extensive cross-validation and randomization testing. Comparison of model prediction with imposed random correlation demonstrated biologic relevance of the model and the reduction of overfitting in DF. Furthermore, two confidence levels (high and low confidences) were assigned to each prediction, where most misclassifications were associated with the low-confidence region. For the high-confidence prediction, the model achieved 99.2% sensitivity and 98.2% specificity. The model also identified a list of significant peaks that could be useful for biomarker identification. DF should be equally applicable to other omics data such as gene expression data or metabolomic data. The DF algorithm is available upon request.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-10618406, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-11108479, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-11381113, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-11385503, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-11934738, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-11983868, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12097261, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12117794, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12324514, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12454645, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12509396, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12642676, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12653524, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12869696, http://linkedlifedata.com/resource/pubmed/commentcorrection/15598613-12881441
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Nov
pubmed:issn
0091-6765
pubmed:author
pubmed:issnType
Print
pubmed:volume
112
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1622-7
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence.
pubmed:affiliation
Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research/FDA, 3900 NCTR Road, HFT020, Jefferson, AK 72079, USA. wtong@nctr.fda.gov
pubmed:publicationType
Journal Article, Evaluation Studies