art%3A10.1186%2F1471-2105-12-S7-A19
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MEETING ABSTRACT Open Access Statistical analysis of microarray gene expression data from a mouse model of toxoplasmosis Shrikant Pawar 1,2* , Cheryl D Davis 1,2 , Claire A Rinehart 1,2 From 10 th Annual UT-ORNL-KBRIN Bioinformatics Summit 2011 Memphis, TN, USA. 1-3 April 2011 Background Toxoplasmosis, caused by the protozoan parasite Toxo- plasma gondii is a major cause of morbidity and mortal- ity in patients with AIDS and an important cause of miscarriage, stillbirth and congenital disease in new- borns. Previous studies have provided evidence that dietary supplementation with vitamin E and selenium is harmful during experimental toxoplasmosis in mice, whereas a diet deficient in vitamin E and selenium results in decreased numbers of tissue cysts in the brain and dramatically reduced brain pathology. The overall goal of the present study was to determine the impact of dietary supplementation with antioxidants on gene expression in the brains of non-infected mice and in mice infected with T. gondii using microarray analysis. RNA was isolated from the brains of C57BL/6 mice, and an Agilent Oligo Whole Mouse Genome Microarray (Agilent Technologies, Inc.) was performed. A total of 48 chips were normalized by Z ratios and the Data Dri- ven Harr Fisch Normalization methods. Differentially expressed genes were identified by applying thresholds to identify significant values and the results were com- pared between the normalization methods. These differ- entially expressed genes and their respective fold change ratios were used in Ingenuity Pathway Analysis (IPA) software to analyze the pathways involved with these genes. Acknowledgements Support from the National Center for Research Resources NIH Grant Number 2 P20 RR-16481 and from the WKU Bioinformatics and Information Science Center is gratefully acknowledged. Author details 1 Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA. 2 Bioinformatics and Information Science Center, Western Kentucky University, Bowling Green, KY 42101, USA. Published: 5 August 2011 doi:10.1186/1471-2105-12-S7-A19 Cite this article as: Pawar et al.: Statistical analysis of microarray gene expression data from a mouse model of toxoplasmosis. BMC Bioinformatics 2011 12(Suppl 7):A19. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit * Correspondence: [email protected] 1 Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA Full list of author information is available at the end of the article Pawar et al. BMC Bioinformatics 2011, 12(Suppl 7):A19 http://www.biomedcentral.com/1471-2105/12/S7/A19 © 2011 Pawar et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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MEETING ABSTRACT Open Access
Statistical analysis of microarray gene expressiondata from a mouse model of toxoplasmosisShrikant Pawar1,2*, Cheryl D Davis1,2, Claire A Rinehart1,2
From 10th Annual UT-ORNL-KBRIN Bioinformatics Summit 2011Memphis, TN, USA. 1-3 April 2011
BackgroundToxoplasmosis, caused by the protozoan parasite Toxo-plasma gondii is a major cause of morbidity and mortal-ity in patients with AIDS and an important cause ofmiscarriage, stillbirth and congenital disease in new-borns. Previous studies have provided evidence thatdietary supplementation with vitamin E and selenium isharmful during experimental toxoplasmosis in mice,whereas a diet deficient in vitamin E and seleniumresults in decreased numbers of tissue cysts in the brainand dramatically reduced brain pathology. The overallgoal of the present study was to determine the impactof dietary supplementation with antioxidants on geneexpression in the brains of non-infected mice and inmice infected with T. gondii using microarray analysis.RNA was isolated from the brains of C57BL/6 mice, andan Agilent Oligo Whole Mouse Genome Microarray(Agilent Technologies, Inc.) was performed. A total of48 chips were normalized by Z ratios and the Data Dri-ven Harr Fisch Normalization methods. Differentiallyexpressed genes were identified by applying thresholdsto identify significant values and the results were com-pared between the normalization methods. These differ-entially expressed genes and their respective fold changeratios were used in Ingenuity Pathway Analysis (IPA)software to analyze the pathways involved with thesegenes.
AcknowledgementsSupport from the National Center for Research Resources NIH Grant Number2 P20 RR-16481 and from the WKU Bioinformatics and Information ScienceCenter is gratefully acknowledged.
Author details1Department of Biology, Western Kentucky University, Bowling Green, KY42101, USA. 2Bioinformatics and Information Science Center, WesternKentucky University, Bowling Green, KY 42101, USA.
Published: 5 August 2011
doi:10.1186/1471-2105-12-S7-A19Cite this article as: Pawar et al.: Statistical analysis of microarray geneexpression data from a mouse model of toxoplasmosis. BMCBioinformatics 2011 12(Suppl 7):A19.
Submit your next manuscript to BioMed Centraland take full advantage of:
• Convenient online submission
• Thorough peer review
• No space constraints or color figure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at www.biomedcentral.com/submit
* Correspondence: [email protected] of Biology, Western Kentucky University, Bowling Green, KY42101, USAFull list of author information is available at the end of the article
Pawar et al. BMC Bioinformatics 2011, 12(Suppl 7):A19http://www.biomedcentral.com/1471-2105/12/S7/A19
© 2011 Pawar et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited.
