The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines

[1]  R. Stallings,et al.  Correction: Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes , 2007, Genome Biology.

[2]  Adrian L. Harris,et al.  Hypoxia — a key regulatory factor in tumour growth , 2002, Nature Reviews Cancer.

[3]  Cesare Furlanello,et al.  Algebraic stability indicators for ranked lists in molecular profiling , 2008, Bioinform..

[4]  Todd L Davidson,et al.  Hypoxic stress induces dimethylated histone H3 lysine 9 through histone methyltransferase G9a in mammalian cells. , 2006, Cancer research.

[5]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[6]  G. Semenza,et al.  Transcriptional regulation of vascular endothelial cell responses to hypoxia by HIF-1. , 2005, Blood.

[7]  R. Altman,et al.  Investigating hypoxic tumor physiology through gene expression patterns , 2003, Oncogene.

[8]  P. Carmeliet,et al.  Role of HIF-1α in hypoxia-mediated apoptosis, cell proliferation and tumour angiogenesis , 1998, Nature.

[9]  Pedro Larrañaga,et al.  A review of feature selection techniques in bioinformatics , 2007, Bioinform..

[10]  Lorenzo Rosasco,et al.  Elastic-net regularization in learning theory , 2008, J. Complex..

[11]  K. Suk,et al.  Identification of the Hypoxia-Inducible Factor 1α-Responsive HGTD-P Gene as a Mediator in the Mitochondrial Apoptotic Pathway , 2004, Molecular and Cellular Biology.

[12]  Wei-Yin Loh,et al.  Classification and regression trees , 2011, WIREs Data Mining Knowl. Discov..

[13]  G. Semenza,et al.  Hypoxia-inducible factor 1: oxygen homeostasis and disease pathophysiology. , 2001, Trends in molecular medicine.

[14]  L. Poellinger,et al.  Hypoxia alters gene expression in human neuroblastoma cells toward an immature and neural crest-like phenotype , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Luigi Varesio,et al.  Hypoxia Modifies the Transcriptome of Primary Human Monocytes: Modulation of Novel Immune-Related Genes and Identification Of CC-Chemokine Ligand 20 as a New Hypoxia-Inducible Gene1 , 2006, The Journal of Immunology.

[16]  Sayan Mukherjee,et al.  Feature Selection for SVMs , 2000, NIPS.

[17]  R. Johnson,et al.  Gene expression profiling of the hypoxia signaling pathway in hypoxia-inducible factor 1alpha null mouse embryonic fibroblasts. , 2003, Gene expression.

[18]  Yoav Freund,et al.  A decision-theoretic generalization of on-line learning and an application to boosting , 1997, EuroCOLT.

[19]  E. Sausville,et al.  Flavopiridol, a protein kinase inhibitor, down-regulates hypoxic induction of vascular endothelial growth factor expression in human monocytes. , 1999, Cancer research.

[20]  G. Semenza.  Targeting HIF-1 for cancer therapy , 2003, Nature Reviews Cancer.

[21]  Li Zhang,et al.  Gene expression profiling reveals the profound upregulation of hypoxia-responsive genes in primary human astrocytes. , 2006, Physiological genomics.

[22]  G. Semenza,et al.  HIF-1-mediated expression of pyruvate dehydrogenase kinase: a metabolic switch required for cellular adaptation to hypoxia. , 2006, Cell metabolism.

[23]  G. Camenisch,et al.  Integration of Oxygen Signaling at the Consensus HRE , 2005, Science's STKE.

[24]  J. Klco,et al.  Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways. , 2003, Molecular cancer research : MCR.

[25]  E. Fredlund,et al.  Transcriptional adaptation of neuroblastoma cells to hypoxia. , 2008, Biochemical and biophysical research communications.

[26]  A. Sica,et al.  A hypoxia-responsive element mediates a novel pathway of activation of the inducible nitric oxide synthase promoter , 1995, The Journal of experimental medicine.

[27]  Sang Chul Park,et al.  Analysis of the effect of aging on the response to hypoxia by cDNA microarray , 2003, Mechanisms of Ageing and Development.

[28]  J. Friedman.  Special Invited Paper-Additive logistic regression: A statistical view of boosting , 2000 .

[29]  Cesare Furlanello,et al.  Entropy-based gene ranking without selection bias for the predictive classification of microarray data , 2003, BMC Bioinformatics.

[30]  Bernhard Schölkopf,et al.  Use of the Zero-Norm with Linear Models and Kernel Methods , 2003, J. Mach. Learn. Res..

[31]  C Caux,et al.  Immunobiology of dendritic cells. , 2000, Annual review of immunology.

[32]  Pat Langley,et al.  Selection of Relevant Features and Examples in Machine Learning , 1997, Artif. Intell..

[33]  P. Thibault,et al.  Transcription Factor HIF-1 Is a Necessary Mediator of the Pasteur Effect in Mammalian Cells , 2001, Molecular and Cellular Biology.

[34]  Johan Vallon-Christersson,et al.  Human neuroblastoma cells exposed to hypoxia: induction of genes associated with growth, survival, and aggressive behavior. , 2004, Experimental cell research.

[35]  Geoffrey J McLachlan,et al.  Selection bias in gene extraction on the basis of microarray gene-expression data , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[37]  George Forman,et al.  An Extensive Empirical Study of Feature Selection Metrics for Text Classification , 2003, J. Mach. Learn. Res..

[38]  E. Merello,et al.  Hypoxia transcriptionally induces macrophage‐inflammatory protein‐3α/CCL‐20 in primary human mononuclear phagocytes through nuclear factor (NF)‐κB , 2008 .

[39]  R. Johnson,et al.  Gene expression profiling of the hypoxia signaling pathway in hypoxia-inducible factor 1alpha null mouse embryonic fibroblasts. , 2003, Gene expression.

[40]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[41]  B. Wouters,et al.  Control of the hypoxic response through regulation of mRNA translation. , 2005, Seminars in cell & developmental biology.

[42]  Stan Z. Li,et al.  FloatBoost learning and statistical face detection , 2004, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[43]  C. Ball,et al.  Repeatability of published microarray gene expression analyses , 2009, Nature Genetics.

[44]  M Schwab,et al.  N‐myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis , 2001, The EMBO journal.

[45]  P. Ratcliffe,et al.  Identification of hypoxically inducible mRNAs in HeLa cells using differential-display PCR. Role of hypoxia-inducible factor-1. , 1996, European journal of biochemistry.

[46]  S. Pastorino,et al.  Engineering of macrophages to produce IFN-gamma in response to hypoxia. , 2001, Journal of immunology.

[47]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[48]  Francesca Odone,et al.  Feature selection for high-dimensional data , 2009, Comput. Manag. Sci..

[49]  E. Merello,et al.  Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB. , 2008, Journal of leukocyte biology.

[50]  S. Cohn,et al.  Advances in the diagnosis and treatment of neuroblastoma , 1998, Current opinion in oncology.

[51]  G. Semenza,et al.  HIF-1 and tumor progression: pathophysiology and therapeutics. , 2002, Trends in molecular medicine.

[52]  A. Elia,et al.  Transcriptome of Hypoxic Immature Dendritic Cells: Modulation of Chemokine/Receptor Expression , 2008, Molecular Cancer Research.

[53]  Trevor Hastie,et al.  Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers , 2006, PLoS medicine.

[54]  Alessandro Verri,et al.  A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data , 2008, J. Comput. Biol..

[55]  Lorenzo Rosasco,et al.  A method for robust variable selection with significance assessment , 2008, ESANN.

[56]  A. Harris,et al.  The expression and distribution of the hypoxia-inducible factors HIF-1α and HIF-2α in normal human tissues, cancers, and tumor-associated macrophages , 2000 .

[57]  Ulrike von Luxburg,et al.  A tutorial on spectral clustering , 2007, Stat. Comput..

[58]  S. Pastorino,et al.  Engineering of Macrophages to Produce IFN-γ in Response to Hypoxia1 , 2001, The Journal of Immunology.

[59]  S. Pastorino,et al.  Flavopiridol inhibits vascular endothelial growth factor production induced by hypoxia or picolinic acid in human neuroblastoma , 2002, International journal of cancer.

[60]  Ron Kohavi,et al.  Irrelevant Features and the Subset Selection Problem , 1994, ICML.

[61]  Ashutosh Kumar Singh,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2010 .

[62]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .