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Significant Analysis of Microarray (SAM) to Identify Synergistic Effect of RV and NGF in Repairing Damaged Neuronal Cells


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1 Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow - 226028, Uttar Pradesh, India
     

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Neurodevelopmental disorders include diseases that are related with genetic disorders and are caused due to stress condition or environmental toxins during pre or post natal condition. In recent years, there is considerable research in neurodevelopmental disorders and examining therapeutic role of resveratrol as potential antioxidant. There is less information about the genes that are mutated or altered during neurodevelopmental phase and cause neuronal developmental disorders. Current researches are evidentially showing the therapeutic potential of Resveratrol (RV) and Nerve Growth Factor (NGF) against neuronal diseases. In current study Microarray experiment was designed to identify the genes that are altered when Mesenchymal Stem Cells (MSC) were exposed to Monocrotophos (MCP). MSCs were also coexposed with resveratrol and nerve growth factor to study the synergistic effect of NGF with RV. Computational analysis of microarray data was carried out through different software’s and bioinformatics tools to identify genes that are expressed in different samples across microarray experiment. Statistical methods like T-test, SAM analysis and clustering techniques were performed between different samples using MeV software. Through Significant Analysis of Microarray (SAM) method we identified positive and negative significant genes with respect to current study. Clustering method was used to cluster genes associated with neuronal disease genes. Key genes that were predicted on the basis of t-test and SAM analysis are DNMT1, PGAP1, RDX and PEX26 genes, these genes have noticeable function in different classes of neuronal diseases like cerebellar ataxia, deafness, narcolepsy, mental retardation and zellweger spectrum disorder etc. Cluster analysis we identified genes such as ATP6V0D1, TESMIN, TRIM22, NAPEPLD, CDK7 and PKM, these genes have important function in cell growth, cell proliferation, protein synthesis, cell cycle regulation, and cell signaling. Study suggests that exposure of damaged neuronal cells to RV and NGF enhances the expression of neuronal repair genes, thus signifies the neuroprotectant and synergistic activity of RV and NGF. “The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus database and are accessible through GEO Series accession number GSE121261 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121261).”

Keywords

Microarray Analysis, Nerve Growth Factor, Neuronal Damage, Neuronal Diseases, Resveratrol, SAM.
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  • Significant Analysis of Microarray (SAM) to Identify Synergistic Effect of RV and NGF in Repairing Damaged Neuronal Cells

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Authors

Ruchi Yadav
Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow - 226028, Uttar Pradesh, India
Prachi Srivastava
Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow - 226028, Uttar Pradesh, India

Abstract


Neurodevelopmental disorders include diseases that are related with genetic disorders and are caused due to stress condition or environmental toxins during pre or post natal condition. In recent years, there is considerable research in neurodevelopmental disorders and examining therapeutic role of resveratrol as potential antioxidant. There is less information about the genes that are mutated or altered during neurodevelopmental phase and cause neuronal developmental disorders. Current researches are evidentially showing the therapeutic potential of Resveratrol (RV) and Nerve Growth Factor (NGF) against neuronal diseases. In current study Microarray experiment was designed to identify the genes that are altered when Mesenchymal Stem Cells (MSC) were exposed to Monocrotophos (MCP). MSCs were also coexposed with resveratrol and nerve growth factor to study the synergistic effect of NGF with RV. Computational analysis of microarray data was carried out through different software’s and bioinformatics tools to identify genes that are expressed in different samples across microarray experiment. Statistical methods like T-test, SAM analysis and clustering techniques were performed between different samples using MeV software. Through Significant Analysis of Microarray (SAM) method we identified positive and negative significant genes with respect to current study. Clustering method was used to cluster genes associated with neuronal disease genes. Key genes that were predicted on the basis of t-test and SAM analysis are DNMT1, PGAP1, RDX and PEX26 genes, these genes have noticeable function in different classes of neuronal diseases like cerebellar ataxia, deafness, narcolepsy, mental retardation and zellweger spectrum disorder etc. Cluster analysis we identified genes such as ATP6V0D1, TESMIN, TRIM22, NAPEPLD, CDK7 and PKM, these genes have important function in cell growth, cell proliferation, protein synthesis, cell cycle regulation, and cell signaling. Study suggests that exposure of damaged neuronal cells to RV and NGF enhances the expression of neuronal repair genes, thus signifies the neuroprotectant and synergistic activity of RV and NGF. “The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus database and are accessible through GEO Series accession number GSE121261 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121261).”

Keywords


Microarray Analysis, Nerve Growth Factor, Neuronal Damage, Neuronal Diseases, Resveratrol, SAM.

References





DOI: https://doi.org/10.18311/ti%2F2018%2F22527