TY - GEN
T1 - Outlier gene set analysis combined with top scoring pair provides robust biomarkers of pathway activity
AU - Ochs, Michael F.
AU - Farrar, Jason E.
AU - Considine, Michael
AU - Wei, Yingying
AU - Meschinchi, Soheil
AU - Arceci, Robert J.
PY - 2013
Y1 - 2013
N2 - Cancer is a disease driven by pathway activity, while useful biomarkers to predict outcome (prognostic markers) or determine treatment (treatment markers) rely on individual genes, proteins, or metabolites. We provide a novel approach that isolates pathways of interest by integrating outlier analysis and gene set analysis and couple it to the top-scoring pair algorithm to identify robust biomarkers. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed AML tumors.
AB - Cancer is a disease driven by pathway activity, while useful biomarkers to predict outcome (prognostic markers) or determine treatment (treatment markers) rely on individual genes, proteins, or metabolites. We provide a novel approach that isolates pathways of interest by integrating outlier analysis and gene set analysis and couple it to the top-scoring pair algorithm to identify robust biomarkers. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed AML tumors.
UR - http://www.scopus.com/inward/record.url?scp=84880757418&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84880757418&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-39159-0-5
DO - 10.1007/978-3-642-39159-0-5
M3 - Conference contribution
AN - SCOPUS:84880757418
SN - 9783642391583
VL - 7986 LNBI
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 47
EP - 58
BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
T2 - 8th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2013
Y2 - 17 June 2013 through 20 June 2013
ER -