Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction
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...
| Main Authors: | , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Hindawi
2011
|
| Online Access: | http://hdl.handle.net/1721.1/61340 https://orcid.org/0000-0001-6376-4786 |
| _version_ | 1811096225624096768 |
|---|---|
| author | Rosasco, Lorenzo Andrea Fardin, Paolo Cornero, Andrea Barla, Annalisa Mosci, Sofia Acquaviva, Massimo Gambini, Claudio Verri, Alessandro Varesio, Luigi |
| author2 | Massachusetts Institute of Technology. Center for Biological & Computational Learning |
| author_facet | Massachusetts Institute of Technology. Center for Biological & Computational Learning Rosasco, Lorenzo Andrea Fardin, Paolo Cornero, Andrea Barla, Annalisa Mosci, Sofia Acquaviva, Massimo Gambini, Claudio Verri, Alessandro Varesio, Luigi |
| author_sort | Rosasco, Lorenzo Andrea |
| collection | MIT |
| description | 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[subscript 1]-l[subscript 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[subscript 1]-l[subscript 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. |
| first_indexed | 2024-09-23T16:40:34Z |
| format | Article |
| id | mit-1721.1/61340 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:40:34Z |
| publishDate | 2011 |
| publisher | Hindawi |
| record_format | dspace |
| spelling | mit-1721.1/613402022-09-29T20:41:54Z Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l [subscript 1]-l subscript 2] Regularization and Data Reduction Rosasco, Lorenzo Andrea Fardin, Paolo Cornero, Andrea Barla, Annalisa Mosci, Sofia Acquaviva, Massimo Gambini, Claudio Verri, Alessandro Varesio, Luigi Massachusetts Institute of Technology. Center for Biological & Computational Learning McGovern Institute for Brain Research at MIT Rosasco, Lorenzo Andrea Rosasco, Lorenzo Andrea 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[subscript 1]-l[subscript 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[subscript 1]-l[subscript 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. Fondazione Italiana per la Lotta al Neuroblastoma Italian Association for Cancer Research (AIRC) Italian Ministry of Health EU Integrated Project Health-e-Child (IST-2004-027749) Compagnia di San Paolo (Foundation) (Project 4998- ID/CV 2007.0887) 2011-02-24T22:52:20Z 2011-02-24T22:52:20Z 2010-04 2010-02 Article http://purl.org/eprint/type/JournalArticle 1110-7243 http://hdl.handle.net/1721.1/61340 Fardin, Paolo et al. “Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l1-l2 Regularization and Data Reduction.” Journal of Biomedicine and Biotechnology 2010 (2010): 1-12. https://orcid.org/0000-0001-6376-4786 en_US http://dx.doi.org/10.1155/2010/878709 Journal of Biomedicine and Biotechnology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0/ application/pdf Hindawi Hindawi |
| spellingShingle | Rosasco, Lorenzo Andrea Fardin, Paolo Cornero, Andrea Barla, Annalisa Mosci, Sofia Acquaviva, Massimo Gambini, Claudio Verri, Alessandro Varesio, Luigi Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title | Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title_full | Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title_fullStr | Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title_full_unstemmed | Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title_short | Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l(1)-l(2) Regularization and Data Reduction |
| title_sort | identification of multiple hypoxia signatures in neuroblastoma cell lines by l 1 l 2 regularization and data reduction |
| url | http://hdl.handle.net/1721.1/61340 https://orcid.org/0000-0001-6376-4786 |
| work_keys_str_mv | AT rosascolorenzoandrea identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT fardinpaolo identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT corneroandrea identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT barlaannalisa identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT moscisofia identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT acquavivamassimo identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT gambiniclaudio identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT verrialessandro identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT varesioluigi identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbyl1l2regularizationanddatareduction AT rosascolorenzoandrea identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT fardinpaolo identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT corneroandrea identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT barlaannalisa identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT moscisofia identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT acquavivamassimo identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT gambiniclaudio identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT verrialessandro identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction AT varesioluigi identificationofmultiplehypoxiasignaturesinneuroblastomacelllinesbylsubscript1lsubscript2regularizationanddatareduction |