Identification of multiple hypoxia signatures in neuroblastoma cell lines by l1-l2 regularization and data reduction.

Journal of Biomedicine & Biotechnology
Paolo FardinLuigi Varesio

Abstract

Hypoxia is a condition of low oxygen tension occurring in the tumor and negatively correlated with the progression of the disease. We studied the gene expression profiles of nine neuroblastoma cell lines grown under hypoxic conditions to define gene signatures that characterize hypoxic neuroblastoma. The l(1)-l(2) regularization applied to the entire transcriptome identified a single signature of 11 probesets discriminating the hypoxic state. We demonstrate that new hypoxia signatures, with similar discriminatory power, can be generated by a prior knowledge-based filtering in which a much smaller number of probesets, characterizing hypoxia-related biochemical pathways, are analyzed. l(1)-l(2) regularization identified novel and robust hypoxia signatures within apoptosis, glycolysis, and oxidative phosphorylation Gene Ontology classes. We conclude that the filtering approach overcomes the noisy nature of the microarray data and allows generating robust signatures suitable for biomarker discovery and patients risk assessment in a fraction of computer time.

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Citations

Jul 17, 2013·BMC Bioinformatics·Davide CangelosiLuigi Varesio
May 10, 2012·Journal of Biomedicine & Biotechnology·Varaprasad KollaSinuhe Hahn
Aug 19, 2015·Journal of Pharmacological and Toxicological Methods·Mandeep Singh KapoorSurendra H Bodakhe
Mar 18, 2016·British Journal of Cancer·Liat Edry BotzerIsaac P Witz
Apr 5, 2013·International Journal of Proteomics·Hung V TrinhSilvio Hemmi
Jan 12, 2012·Clinical & Developmental Immunology·Wenbao ZhangDonald P McManus
Feb 13, 2013·International Journal of Proteomics·Alessandra TessitoreEdoardo Alesse
Mar 27, 2012·PPAR Research·Eugenia HovsepianNora B Goren
Jan 1, 2012·International Journal of Medicinal Chemistry·Marina RoussakiAnastasia Detsi
Oct 25, 2012·Journal of Biomedicine & Biotechnology·Xin YongShi-Ming Yang
Jan 21, 2012·Journal of Biomedicine & Biotechnology·T P Velavan, Olusola Ojurongbe
Jul 1, 2011·Journal of Biomedicine & Biotechnology·Qian WuQinyu Ge
Feb 12, 2017·BMC Bioinformatics·Davide CangelosiLuigi Varesio
Oct 24, 2017·Journal of Cellular Physiology·Mattia CriscuoliAntonella Naldini

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Datasets Mentioned

BETA
GSE15583

Methods Mentioned

BETA
PCA
chip

Software Mentioned

Ensembl
MATLAB Statistic Toolbox
Ensembl Perl APIs
Genomatix
Bioconductor
affy
R script
MatInspector
GeneSpring
MATLAB

Related Concepts

Related Feeds

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis