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Article: Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells

TitleRemoving intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells
Authors
Issue Date2005
PublisherNational Academy of Sciences. The Journal's web site is located at http://www.pnas.org
Citation
Proceedings of the National Academy of Sciences of the United States of America (PNAS), 2005, v. 102 n. 49, p. 17751-17756 How to Cite?
AbstractA Semilinear In-Slide Model Is Introduced To Remove The Intensity Effect In The Scanning Process. It Is Demonstrated That The Intensity Effect Can Be Estimated Accurately And Removed Effectively. This Normalization Step Is Vital For Affymetrix Arrays To Reveal Relevant Biological Results When Comparing Gene Expression In Multiple Arrays. The Normalized Expression Ratios Are Analyzed Further By A Modified Two-Sample T Test Along With A Sieved Permutation Scheme For Computing P Values. The Improved Specificity And Sensitivity Are Demonstrated By Using A Study On The Impact Of Macrophage Migration Inhibitory Factor (Mif) Reduction In Neuroblastoma Cells. With Semilinear In-Slide Model Analysis, Expression Of 166 Genes Was Altered With A P Value No Greater Than 0.001. Among Those Genes, 44 Were Altered >2-Fold. Mif-Regulated Genes Associated With Tumor Development Including Il-8 And C-Met, Which Are Overexpressed In Many Tumors, Were Down-Regulated In Mif-Reduced Cells. On The Other Hand, Some Tumor-Suppressor Genes Such As Ephb6, Visinin-Like Protein 1 (Vsnl-1), And Blu Were Up-Regulated In Mif-Reduced Cells. In Addition, We Demonstrated That Down-Regulation Of Mif Expression Could Result In A Reduction In Cell Proliferation And Tumor Growth In Vitro And In Vivo. Our Data Not Only Demonstrate That Targeting Mif Expression Is A Promising Therapeutic Strategy In Human Neuroblastoma Therapy But Also Indicate The Mif Target Genes For Additional Study. © 2005 By The National Academy Of Sciences Of The Usa.
Persistent Identifierhttp://hdl.handle.net/10722/83593
ISSN
2015 Impact Factor: 9.423
2015 SCImago Journal Rankings: 6.883
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorFan, JQen_HK
dc.contributor.authorChen, Yen_HK
dc.contributor.authorChan, HMen_HK
dc.contributor.authorTam, PKHen_HK
dc.contributor.authorRen, Yen_HK
dc.date.accessioned2010-09-06T08:42:52Z-
dc.date.available2010-09-06T08:42:52Z-
dc.date.issued2005en_HK
dc.identifier.citationProceedings of the National Academy of Sciences of the United States of America (PNAS), 2005, v. 102 n. 49, p. 17751-17756en_HK
dc.identifier.issn0027-8424en_US
dc.identifier.urihttp://hdl.handle.net/10722/83593-
dc.description.abstractA Semilinear In-Slide Model Is Introduced To Remove The Intensity Effect In The Scanning Process. It Is Demonstrated That The Intensity Effect Can Be Estimated Accurately And Removed Effectively. This Normalization Step Is Vital For Affymetrix Arrays To Reveal Relevant Biological Results When Comparing Gene Expression In Multiple Arrays. The Normalized Expression Ratios Are Analyzed Further By A Modified Two-Sample T Test Along With A Sieved Permutation Scheme For Computing P Values. The Improved Specificity And Sensitivity Are Demonstrated By Using A Study On The Impact Of Macrophage Migration Inhibitory Factor (Mif) Reduction In Neuroblastoma Cells. With Semilinear In-Slide Model Analysis, Expression Of 166 Genes Was Altered With A P Value No Greater Than 0.001. Among Those Genes, 44 Were Altered >2-Fold. Mif-Regulated Genes Associated With Tumor Development Including Il-8 And C-Met, Which Are Overexpressed In Many Tumors, Were Down-Regulated In Mif-Reduced Cells. On The Other Hand, Some Tumor-Suppressor Genes Such As Ephb6, Visinin-Like Protein 1 (Vsnl-1), And Blu Were Up-Regulated In Mif-Reduced Cells. In Addition, We Demonstrated That Down-Regulation Of Mif Expression Could Result In A Reduction In Cell Proliferation And Tumor Growth In Vitro And In Vivo. Our Data Not Only Demonstrate That Targeting Mif Expression Is A Promising Therapeutic Strategy In Human Neuroblastoma Therapy But Also Indicate The Mif Target Genes For Additional Study. © 2005 By The National Academy Of Sciences Of The Usa.en_US
dc.languageengen_HK
dc.publisherNational Academy of Sciences. The Journal's web site is located at http://www.pnas.orgen_US
dc.relation.ispartofProceedings of the National Academy of Sciences of the United States of America (PNAS)en_HK
dc.titleRemoving intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cellsen_HK
dc.typeArticleen_HK
dc.identifier.emailTam, PKH: paultam@hkucc.hku.hken_HK
dc.identifier.emailRen, Y: yren@hkucc.hku.hken_HK
dc.identifier.authorityTam, PKH=rp00060en_HK
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1073/pnas.0509175102en_US
dc.identifier.pmid16314559-
dc.identifier.pmcidPMC1308934-
dc.identifier.scopuseid_2-s2.0-29144463142en_US
dc.identifier.hkuros112002en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-29144463142&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume102en_US
dc.identifier.issue49en_US
dc.identifier.spage17751en_US
dc.identifier.epage17756en_US
dc.identifier.isiWOS:000233849000039-
dc.identifier.citeulike1903363-

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